Starting phenix.real_space_refine on Wed Jul 23 14:34:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yh6_33820/07_2025/7yh6_33820.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yh6_33820/07_2025/7yh6_33820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yh6_33820/07_2025/7yh6_33820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yh6_33820/07_2025/7yh6_33820.map" model { file = "/net/cci-nas-00/data/ceres_data/7yh6_33820/07_2025/7yh6_33820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yh6_33820/07_2025/7yh6_33820.cif" } resolution = 3.4 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= 0.001 sd= 0.008 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 14 5.16 5 C 2121 2.51 5 N 563 2.21 5 O 645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3343 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 823 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "H" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "A" 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: "A" 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: 6.26, per 1000 atoms: 1.87 Number of scatterers: 3343 At special positions: 0 Unit cell: (58.29, 75.04, 97.82, 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 14 16.00 O 645 8.00 N 563 7.00 C 2121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 441.0 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 11.9% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'L' and resid 81 through 85 removed outlier: 4.081A pdb=" N ASP L 84 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU L 85 " --> pdb=" O THR L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.281A pdb=" N THR H 91 " --> pdb=" O PRO H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.657A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.504A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.213A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.569A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.805A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.688A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 10 removed outlier: 4.052A pdb=" N ALA L 86 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 9 through 10 removed outlier: 4.052A pdb=" N ALA L 86 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU L 99 " --> pdb=" O ASP L 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.656A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.739A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.517A pdb=" N PHE H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.624A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 102 hydrogen bonds defined for protein. 252 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: 0.94 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1082 1.34 - 1.46: 917 1.46 - 1.58: 1416 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3431 Sorted by residual: bond pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " ideal model delta sigma weight residual 1.534 1.515 0.019 1.77e-02 3.19e+03 1.18e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.427 -0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.10e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.95e-01 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.469 0.029 3.10e-02 1.04e+03 8.84e-01 ... (remaining 3426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 4602 2.27 - 4.55: 58 4.55 - 6.82: 4 6.82 - 9.09: 1 9.09 - 11.37: 2 Bond angle restraints: 4667 Sorted by residual: angle pdb=" N VAL A 524 " pdb=" CA VAL A 524 " pdb=" C VAL A 524 " ideal model delta sigma weight residual 106.42 113.30 -6.88 1.51e+00 4.39e-01 2.07e+01 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 124.22 -9.82 2.30e+00 1.89e-01 1.82e+01 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 109.14 114.72 -5.58 1.49e+00 4.50e-01 1.40e+01 angle pdb=" C THR A 523 " pdb=" N VAL A 524 " pdb=" CA VAL A 524 " ideal model delta sigma weight residual 122.96 120.03 2.93 9.50e-01 1.11e+00 9.50e+00 angle pdb=" N VAL A 524 " pdb=" CA VAL A 524 " pdb=" CB VAL A 524 " ideal model delta sigma weight residual 112.65 109.98 2.67 1.00e+00 1.00e+00 7.12e+00 ... (remaining 4662 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 1809 17.61 - 35.22: 175 35.22 - 52.83: 25 52.83 - 70.44: 5 70.44 - 88.05: 3 Dihedral angle restraints: 2017 sinusoidal: 785 harmonic: 1232 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 2.05 -88.05 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -121.23 35.23 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 2014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 352 0.046 - 0.092: 103 0.092 - 0.138: 40 0.138 - 0.184: 0 0.184 - 0.230: 2 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA CYS A 391 " pdb=" N CYS A 391 " pdb=" C CYS A 391 " pdb=" CB CYS A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB THR A 430 " pdb=" CA THR A 430 " pdb=" OG1 THR A 430 " pdb=" CG2 THR A 430 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE L 20 " pdb=" N ILE L 20 " pdb=" C ILE L 20 " pdb=" CB ILE L 20 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 494 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 60 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO L 61 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.012 2.00e-02 2.50e+03 1.11e-02 1.54e+00 pdb=" CG ASN A 343 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.011 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 347 " 0.010 2.00e-02 2.50e+03 8.56e-03 1.28e+00 pdb=" CG PHE A 347 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A 347 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 347 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 347 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 347 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 347 " 0.001 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 128 2.71 - 3.26: 3160 3.26 - 3.80: 4834 3.80 - 4.35: 5934 4.35 - 4.90: 10656 Nonbonded interactions: 24712 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" OE2 GLU A 516 " model vdw 2.161 3.040 nonbonded pdb=" O PHE H 29 " pdb=" NH2 ARG H 72 " model vdw 2.237 3.120 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.257 3.040 nonbonded pdb=" OG SER H 17 " pdb=" O MET H 83 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.280 3.040 ... (remaining 24707 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.020 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3438 Z= 0.202 Angle : 0.657 11.365 4682 Z= 0.332 Chirality : 0.048 0.230 497 Planarity : 0.004 0.036 611 Dihedral : 13.192 80.334 1223 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.08 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.42), residues: 424 helix: -3.28 (0.65), residues: 33 sheet: 0.96 (0.47), residues: 141 loop : -1.15 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 36 HIS 0.004 0.002 HIS H 35 PHE 0.019 0.001 PHE A 347 TYR 0.010 0.001 TYR H 106 ARG 0.006 0.001 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 1) link_NAG-ASN : angle 3.23820 ( 3) hydrogen bonds : bond 0.26985 ( 93) hydrogen bonds : angle 9.47683 ( 252) SS BOND : bond 0.00478 ( 6) SS BOND : angle 2.97969 ( 12) covalent geometry : bond 0.00463 ( 3431) covalent geometry : angle 0.63506 ( 4667) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: H 56 ASN cc_start: 0.9234 (m110) cc_final: 0.8833 (m110) REVERT: H 62 ASP cc_start: 0.8516 (t70) cc_final: 0.8302 (t0) REVERT: H 73 ASP cc_start: 0.8079 (t0) cc_final: 0.7637 (t0) REVERT: H 99 ASP cc_start: 0.8765 (t70) cc_final: 0.8530 (t0) REVERT: A 420 ASP cc_start: 0.8704 (m-30) cc_final: 0.8300 (m-30) REVERT: A 489 TYR cc_start: 0.8761 (m-10) cc_final: 0.8525 (m-10) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1667 time to fit residues: 13.7390 Evaluate side-chains 60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.077884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.057242 restraints weight = 8081.868| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.86 r_work: 0.2585 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3438 Z= 0.125 Angle : 0.621 10.341 4682 Z= 0.314 Chirality : 0.046 0.145 497 Planarity : 0.004 0.039 611 Dihedral : 4.708 33.407 496 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.25 % Favored : 95.28 % Rotamer: Outliers : 0.83 % Allowed : 9.17 % Favored : 90.00 % 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: -0.89 (0.41), residues: 424 helix: -3.34 (0.62), residues: 33 sheet: 0.83 (0.45), residues: 144 loop : -1.10 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 PHE 0.009 0.001 PHE A 392 TYR 0.017 0.001 TYR H 53 ARG 0.002 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 1) link_NAG-ASN : angle 1.73832 ( 3) hydrogen bonds : bond 0.04798 ( 93) hydrogen bonds : angle 6.55603 ( 252) SS BOND : bond 0.00442 ( 6) SS BOND : angle 2.41572 ( 12) covalent geometry : bond 0.00282 ( 3431) covalent geometry : angle 0.60797 ( 4667) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.354 Fit side-chains REVERT: L 85 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7356 (pm20) REVERT: H 43 LYS cc_start: 0.8324 (mmmt) cc_final: 0.8098 (mmmt) REVERT: H 56 ASN cc_start: 0.9293 (m110) cc_final: 0.8925 (m110) REVERT: H 73 ASP cc_start: 0.8058 (t0) cc_final: 0.7619 (t0) REVERT: A 420 ASP cc_start: 0.9059 (m-30) cc_final: 0.8637 (m-30) REVERT: A 489 TYR cc_start: 0.8866 (m-10) cc_final: 0.8663 (m-10) REVERT: A 525 CYS cc_start: 0.6524 (p) cc_final: 0.6303 (p) outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 0.1674 time to fit residues: 14.2147 Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3131 r_free = 0.3131 target = 0.077127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.056606 restraints weight = 8117.817| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.81 r_work: 0.2566 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3438 Z= 0.164 Angle : 0.607 9.465 4682 Z= 0.310 Chirality : 0.046 0.132 497 Planarity : 0.004 0.040 611 Dihedral : 4.414 29.201 496 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.66 % Favored : 94.10 % Rotamer: Outliers : 1.67 % Allowed : 11.94 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.41), residues: 424 helix: -3.13 (0.68), residues: 33 sheet: 0.74 (0.44), residues: 152 loop : -1.19 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.006 0.002 HIS A 519 PHE 0.009 0.001 PHE A 347 TYR 0.018 0.001 TYR H 53 ARG 0.002 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 1) link_NAG-ASN : angle 1.44694 ( 3) hydrogen bonds : bond 0.04480 ( 93) hydrogen bonds : angle 6.14216 ( 252) SS BOND : bond 0.00398 ( 6) SS BOND : angle 2.31832 ( 12) covalent geometry : bond 0.00383 ( 3431) covalent geometry : angle 0.59502 ( 4667) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.381 Fit side-chains REVERT: L 85 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7438 (pm20) REVERT: H 43 LYS cc_start: 0.8264 (mmmt) cc_final: 0.8002 (mmmt) REVERT: H 56 ASN cc_start: 0.9307 (m110) cc_final: 0.8925 (m110) REVERT: H 73 ASP cc_start: 0.7917 (t0) cc_final: 0.7501 (t0) REVERT: H 117 GLN cc_start: 0.9115 (tp40) cc_final: 0.8899 (mm110) REVERT: A 420 ASP cc_start: 0.9066 (m-30) cc_final: 0.8602 (m-30) REVERT: A 489 TYR cc_start: 0.8886 (m-10) cc_final: 0.8649 (m-10) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 0.1468 time to fit residues: 11.6818 Evaluate side-chains 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3142 r_free = 0.3142 target = 0.077661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.056859 restraints weight = 8230.418| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.79 r_work: 0.2576 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3438 Z= 0.155 Angle : 0.598 8.865 4682 Z= 0.304 Chirality : 0.045 0.132 497 Planarity : 0.004 0.041 611 Dihedral : 4.309 26.830 496 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.66 % Favored : 94.10 % Rotamer: Outliers : 1.67 % Allowed : 14.17 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.41), residues: 424 helix: -2.95 (0.72), residues: 33 sheet: 0.68 (0.44), residues: 152 loop : -1.18 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.006 0.002 HIS A 519 PHE 0.010 0.001 PHE L 51 TYR 0.018 0.001 TYR H 53 ARG 0.002 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 1) link_NAG-ASN : angle 1.31971 ( 3) hydrogen bonds : bond 0.04112 ( 93) hydrogen bonds : angle 5.90837 ( 252) SS BOND : bond 0.00370 ( 6) SS BOND : angle 2.24558 ( 12) covalent geometry : bond 0.00364 ( 3431) covalent geometry : angle 0.58723 ( 4667) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.359 Fit side-chains REVERT: L 85 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7532 (pm20) REVERT: H 43 LYS cc_start: 0.8210 (mmmt) cc_final: 0.7970 (mmmt) REVERT: H 56 ASN cc_start: 0.9299 (m110) cc_final: 0.8916 (m110) REVERT: H 73 ASP cc_start: 0.8009 (t0) cc_final: 0.7577 (t0) REVERT: A 420 ASP cc_start: 0.9058 (m-30) cc_final: 0.8567 (m-30) outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 0.1558 time to fit residues: 12.4388 Evaluate side-chains 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.0670 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3157 r_free = 0.3157 target = 0.078448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.057932 restraints weight = 8194.968| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.85 r_work: 0.2596 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3438 Z= 0.105 Angle : 0.560 7.866 4682 Z= 0.285 Chirality : 0.044 0.131 497 Planarity : 0.004 0.042 611 Dihedral : 4.115 25.346 496 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.95 % Favored : 94.81 % Rotamer: Outliers : 1.94 % Allowed : 15.83 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.41), residues: 424 helix: -2.96 (0.72), residues: 33 sheet: 0.71 (0.44), residues: 152 loop : -1.15 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.006 0.001 HIS A 519 PHE 0.009 0.001 PHE L 51 TYR 0.018 0.001 TYR H 53 ARG 0.002 0.000 ARG L 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 1) link_NAG-ASN : angle 1.20722 ( 3) hydrogen bonds : bond 0.03527 ( 93) hydrogen bonds : angle 5.67111 ( 252) SS BOND : bond 0.00321 ( 6) SS BOND : angle 1.93245 ( 12) covalent geometry : bond 0.00237 ( 3431) covalent geometry : angle 0.55105 ( 4667) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.377 Fit side-chains REVERT: L 85 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7532 (pm20) REVERT: H 43 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7881 (mmmt) REVERT: H 56 ASN cc_start: 0.9303 (m110) cc_final: 0.8912 (m110) REVERT: H 73 ASP cc_start: 0.7793 (t0) cc_final: 0.7415 (t0) REVERT: A 420 ASP cc_start: 0.9045 (m-30) cc_final: 0.8548 (m-30) outliers start: 7 outliers final: 4 residues processed: 70 average time/residue: 0.1539 time to fit residues: 13.2076 Evaluate side-chains 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.0070 chunk 29 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 12 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3176 r_free = 0.3176 target = 0.079547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.058880 restraints weight = 8321.434| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.93 r_work: 0.2623 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3438 Z= 0.093 Angle : 0.550 7.048 4682 Z= 0.280 Chirality : 0.044 0.129 497 Planarity : 0.003 0.041 611 Dihedral : 3.910 23.727 496 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.67 % Allowed : 16.67 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.41), residues: 424 helix: -2.99 (0.72), residues: 33 sheet: 0.73 (0.44), residues: 154 loop : -1.05 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.006 0.001 HIS A 519 PHE 0.009 0.001 PHE L 51 TYR 0.017 0.001 TYR H 80 ARG 0.002 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 1) link_NAG-ASN : angle 1.08823 ( 3) hydrogen bonds : bond 0.03213 ( 93) hydrogen bonds : angle 5.49187 ( 252) SS BOND : bond 0.00345 ( 6) SS BOND : angle 1.89755 ( 12) covalent geometry : bond 0.00206 ( 3431) covalent geometry : angle 0.54134 ( 4667) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.349 Fit side-chains REVERT: L 85 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7630 (pm20) REVERT: H 56 ASN cc_start: 0.9306 (m110) cc_final: 0.8925 (m110) REVERT: H 73 ASP cc_start: 0.7864 (t0) cc_final: 0.7439 (t0) REVERT: A 389 ASP cc_start: 0.8896 (m-30) cc_final: 0.8678 (m-30) REVERT: A 420 ASP cc_start: 0.9067 (m-30) cc_final: 0.8583 (m-30) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.1564 time to fit residues: 13.4421 Evaluate side-chains 71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 35 optimal weight: 0.0970 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3164 r_free = 0.3164 target = 0.078796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.058307 restraints weight = 8238.369| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.87 r_work: 0.2607 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3438 Z= 0.115 Angle : 0.589 7.643 4682 Z= 0.296 Chirality : 0.044 0.128 497 Planarity : 0.003 0.041 611 Dihedral : 3.892 22.458 496 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.22 % Allowed : 16.94 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.41), residues: 424 helix: -2.97 (0.73), residues: 33 sheet: 0.76 (0.44), residues: 152 loop : -1.06 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.006 0.001 HIS A 519 PHE 0.009 0.001 PHE L 51 TYR 0.017 0.001 TYR H 53 ARG 0.003 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 1) link_NAG-ASN : angle 1.11494 ( 3) hydrogen bonds : bond 0.03356 ( 93) hydrogen bonds : angle 5.45312 ( 252) SS BOND : bond 0.00388 ( 6) SS BOND : angle 1.97467 ( 12) covalent geometry : bond 0.00270 ( 3431) covalent geometry : angle 0.58065 ( 4667) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.350 Fit side-chains REVERT: L 85 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7661 (pm20) REVERT: H 56 ASN cc_start: 0.9307 (m110) cc_final: 0.8909 (m110) REVERT: H 73 ASP cc_start: 0.7915 (t0) cc_final: 0.7487 (t0) REVERT: A 389 ASP cc_start: 0.8894 (m-30) cc_final: 0.8661 (m-30) REVERT: A 420 ASP cc_start: 0.9064 (m-30) cc_final: 0.8568 (m-30) REVERT: A 489 TYR cc_start: 0.8810 (m-10) cc_final: 0.8560 (m-10) outliers start: 8 outliers final: 5 residues processed: 72 average time/residue: 0.1340 time to fit residues: 12.0559 Evaluate side-chains 71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3153 r_free = 0.3153 target = 0.078154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.057788 restraints weight = 8174.960| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.81 r_work: 0.2596 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3438 Z= 0.142 Angle : 0.617 7.767 4682 Z= 0.310 Chirality : 0.045 0.131 497 Planarity : 0.004 0.040 611 Dihedral : 3.935 21.567 496 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.78 % Allowed : 15.83 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.41), residues: 424 helix: -2.95 (0.73), residues: 33 sheet: 0.84 (0.44), residues: 152 loop : -1.07 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.006 0.002 HIS A 519 PHE 0.009 0.001 PHE L 51 TYR 0.017 0.001 TYR H 53 ARG 0.002 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 1) link_NAG-ASN : angle 1.18750 ( 3) hydrogen bonds : bond 0.03557 ( 93) hydrogen bonds : angle 5.56145 ( 252) SS BOND : bond 0.00397 ( 6) SS BOND : angle 2.23234 ( 12) covalent geometry : bond 0.00336 ( 3431) covalent geometry : angle 0.60673 ( 4667) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.387 Fit side-chains REVERT: L 85 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7654 (pm20) REVERT: H 56 ASN cc_start: 0.9304 (m110) cc_final: 0.8890 (m110) REVERT: H 73 ASP cc_start: 0.7899 (t0) cc_final: 0.7498 (t0) REVERT: A 389 ASP cc_start: 0.8917 (m-30) cc_final: 0.8704 (m-30) REVERT: A 420 ASP cc_start: 0.9059 (m-30) cc_final: 0.8551 (m-30) REVERT: A 489 TYR cc_start: 0.8803 (m-10) cc_final: 0.8572 (m-10) outliers start: 10 outliers final: 8 residues processed: 71 average time/residue: 0.1421 time to fit residues: 12.6511 Evaluate side-chains 74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3148 r_free = 0.3148 target = 0.077946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.057445 restraints weight = 8285.999| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.85 r_work: 0.2588 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3438 Z= 0.148 Angle : 0.641 8.945 4682 Z= 0.320 Chirality : 0.045 0.129 497 Planarity : 0.003 0.040 611 Dihedral : 3.997 20.930 496 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.22 % Allowed : 15.83 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.41), residues: 424 helix: -2.96 (0.73), residues: 33 sheet: 0.87 (0.44), residues: 152 loop : -1.08 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.007 0.002 HIS A 519 PHE 0.009 0.001 PHE L 51 TYR 0.018 0.001 TYR H 53 ARG 0.002 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 1) link_NAG-ASN : angle 1.25585 ( 3) hydrogen bonds : bond 0.03605 ( 93) hydrogen bonds : angle 5.58517 ( 252) SS BOND : bond 0.00385 ( 6) SS BOND : angle 2.14780 ( 12) covalent geometry : bond 0.00352 ( 3431) covalent geometry : angle 0.63208 ( 4667) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.383 Fit side-chains REVERT: L 85 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7682 (pm20) REVERT: H 56 ASN cc_start: 0.9312 (m110) cc_final: 0.8901 (m110) REVERT: H 73 ASP cc_start: 0.7963 (t0) cc_final: 0.7558 (t0) REVERT: A 389 ASP cc_start: 0.8917 (m-30) cc_final: 0.8694 (m-30) REVERT: A 420 ASP cc_start: 0.9068 (m-30) cc_final: 0.8543 (m-30) outliers start: 8 outliers final: 8 residues processed: 69 average time/residue: 0.1408 time to fit residues: 12.0896 Evaluate side-chains 73 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 10.0000 chunk 41 optimal weight: 0.5980 chunk 4 optimal weight: 0.0050 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 0.0870 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.3150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3193 r_free = 0.3193 target = 0.080278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.059957 restraints weight = 8089.074| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.86 r_work: 0.2647 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 3438 Z= 0.101 Angle : 0.621 9.904 4682 Z= 0.308 Chirality : 0.044 0.131 497 Planarity : 0.003 0.040 611 Dihedral : 3.807 20.219 496 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.39 % Allowed : 17.50 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.41), residues: 424 helix: -3.00 (0.72), residues: 33 sheet: 0.94 (0.43), residues: 155 loop : -1.05 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.006 0.001 HIS A 519 PHE 0.009 0.001 PHE L 51 TYR 0.014 0.001 TYR H 53 ARG 0.003 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 1) link_NAG-ASN : angle 1.06149 ( 3) hydrogen bonds : bond 0.02886 ( 93) hydrogen bonds : angle 5.39573 ( 252) SS BOND : bond 0.00280 ( 6) SS BOND : angle 1.77754 ( 12) covalent geometry : bond 0.00229 ( 3431) covalent geometry : angle 0.61483 ( 4667) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.352 Fit side-chains REVERT: L 85 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7593 (pm20) REVERT: H 56 ASN cc_start: 0.9310 (m110) cc_final: 0.8927 (m110) REVERT: H 73 ASP cc_start: 0.8003 (t0) cc_final: 0.7592 (t0) REVERT: A 389 ASP cc_start: 0.8868 (m-30) cc_final: 0.8637 (m-30) REVERT: A 420 ASP cc_start: 0.9048 (m-30) cc_final: 0.8545 (m-30) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.1614 time to fit residues: 13.5316 Evaluate side-chains 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3138 r_free = 0.3138 target = 0.077182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.056999 restraints weight = 8274.470| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.69 r_work: 0.2590 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3438 Z= 0.177 Angle : 0.675 9.949 4682 Z= 0.338 Chirality : 0.046 0.155 497 Planarity : 0.004 0.039 611 Dihedral : 4.044 19.481 496 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.83 % Allowed : 18.33 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.41), residues: 424 helix: -2.92 (0.76), residues: 33 sheet: 0.87 (0.44), residues: 152 loop : -1.08 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.007 0.002 HIS A 519 PHE 0.009 0.001 PHE L 51 TYR 0.019 0.001 TYR H 53 ARG 0.004 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 1) link_NAG-ASN : angle 1.24769 ( 3) hydrogen bonds : bond 0.03847 ( 93) hydrogen bonds : angle 5.56026 ( 252) SS BOND : bond 0.00449 ( 6) SS BOND : angle 2.13195 ( 12) covalent geometry : bond 0.00423 ( 3431) covalent geometry : angle 0.66644 ( 4667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2354.64 seconds wall clock time: 41 minutes 19.91 seconds (2479.91 seconds total)