Starting phenix.real_space_refine on Sun Apr 27 10:03:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsi_38619/04_2025/8xsi_38619.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsi_38619/04_2025/8xsi_38619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xsi_38619/04_2025/8xsi_38619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsi_38619/04_2025/8xsi_38619.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsi_38619/04_2025/8xsi_38619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsi_38619/04_2025/8xsi_38619.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2404 atoms to isotropic. 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 17 5.16 5 C 2124 2.51 5 N 565 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3354 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1549 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Conformer: "B" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} bond proxies already assigned to first conformer: 1580 Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 975 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.94, per 1000 atoms: 1.17 Number of scatterers: 3354 At special positions: 0 Unit cell: (62.9, 76.5, 89.25, 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 17 16.00 O 648 8.00 N 565 7.00 C 2124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 109 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 B 601 " - " ASN B 343 " Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 529.8 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: 780 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 10.0% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.326A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.522A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.897A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.549A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.853A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.544A 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 Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.566A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) 107 hydrogen bonds defined for protein. 255 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: 0.85 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1072 1.35 - 1.48: 973 1.48 - 1.60: 1374 1.60 - 1.72: 0 1.72 - 1.85: 20 Bond restraints: 3439 Sorted by residual: bond pdb=" CB CYS H 109 " pdb=" SG CYS H 109 " ideal model delta sigma weight residual 1.808 1.849 -0.041 3.30e-02 9.18e+02 1.55e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.428 -0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" C5 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" C3 NAG B 601 " pdb=" O3 NAG B 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" CG PRO L 8 " pdb=" CD PRO L 8 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.70e-02 1.37e+03 9.67e-01 ... (remaining 3434 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 4442 1.23 - 2.45: 176 2.45 - 3.68: 42 3.68 - 4.91: 8 4.91 - 6.13: 2 Bond angle restraints: 4670 Sorted by residual: angle pdb=" C SER H 108 " pdb=" N CYS H 109 " pdb=" CA CYS H 109 " ideal model delta sigma weight residual 122.08 125.77 -3.69 1.47e+00 4.63e-01 6.31e+00 angle pdb=" C ALA L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 125.83 -4.29 1.91e+00 2.74e-01 5.05e+00 angle pdb=" C SER L 14 " pdb=" N VAL L 15 " pdb=" CA VAL L 15 " ideal model delta sigma weight residual 120.63 123.54 -2.91 1.33e+00 5.65e-01 4.78e+00 angle pdb=" C LYS H 58 " pdb=" N TYR H 59 " pdb=" CA TYR H 59 " ideal model delta sigma weight residual 122.29 118.73 3.56 1.65e+00 3.67e-01 4.66e+00 angle pdb=" C VAL B 362 " pdb=" N ALA B 363 " pdb=" CA ALA B 363 " ideal model delta sigma weight residual 121.56 124.63 -3.07 1.56e+00 4.11e-01 3.87e+00 ... (remaining 4665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.10: 1831 14.10 - 28.21: 150 28.21 - 42.31: 41 42.31 - 56.41: 9 56.41 - 70.52: 6 Dihedral angle restraints: 2037 sinusoidal: 798 harmonic: 1239 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 36.93 56.07 1 1.00e+01 1.00e-02 4.24e+01 dihedral pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta harmonic sigma weight residual -180.00 -162.52 -17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASN H 74 " pdb=" C ASN H 74 " pdb=" N SER H 75 " pdb=" CA SER H 75 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 2034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 311 0.036 - 0.071: 129 0.071 - 0.107: 36 0.107 - 0.142: 20 0.142 - 0.178: 2 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA CYS H 109 " pdb=" N CYS H 109 " pdb=" C CYS H 109 " pdb=" CB CYS H 109 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA PRO L 44 " pdb=" N PRO L 44 " pdb=" C PRO L 44 " pdb=" CB PRO L 44 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA CYS H 104 " pdb=" N CYS H 104 " pdb=" C CYS H 104 " pdb=" CB CYS H 104 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 495 not shown) Planarity restraints: 605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO L 80 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 521 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 43 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO L 44 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " -0.020 5.00e-02 4.00e+02 ... (remaining 602 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 65 2.69 - 3.24: 2922 3.24 - 3.79: 4850 3.79 - 4.35: 6992 4.35 - 4.90: 11499 Nonbonded interactions: 26328 Sorted by model distance: nonbonded pdb=" OD1 ASN B 354 " pdb=" OG SER B 399 " model vdw 2.136 3.040 nonbonded pdb=" OD2 ASP H 54 " pdb=" OG SER H 56 " model vdw 2.165 3.040 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.268 3.040 nonbonded pdb=" OD1 ASN B 360 " pdb=" OG1 THR B 523 " model vdw 2.272 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.278 3.040 ... (remaining 26323 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 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.130 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.003 0.041 3446 Z= 0.145 Angle : 0.612 6.133 4685 Z= 0.330 Chirality : 0.046 0.178 498 Planarity : 0.004 0.055 604 Dihedral : 12.125 70.517 1239 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 0.55 % Allowed : 0.00 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.70 (0.40), residues: 424 helix: -3.12 (0.78), residues: 24 sheet: 0.52 (0.42), residues: 159 loop : -0.86 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 116 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE B 486 TYR 0.015 0.001 TYR B 495 ARG 0.004 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 1) link_NAG-ASN : angle 1.60260 ( 3) hydrogen bonds : bond 0.16616 ( 102) hydrogen bonds : angle 7.52024 ( 255) SS BOND : bond 0.00464 ( 6) SS BOND : angle 1.92695 ( 12) covalent geometry : bond 0.00316 ( 3439) covalent geometry : angle 0.60428 ( 4670) *********************** 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 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.349 Fit side-chains REVERT: B 370 ASN cc_start: 0.7194 (m-40) cc_final: 0.6819 (m-40) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.7834 time to fit residues: 45.8833 Evaluate side-chains 53 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.0060 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 GLN H 35 HIS H 77 ASN L 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.147275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.129370 restraints weight = 9052.285| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.46 r_work: 0.3771 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3446 Z= 0.207 Angle : 0.652 5.909 4685 Z= 0.349 Chirality : 0.048 0.178 498 Planarity : 0.005 0.057 604 Dihedral : 6.036 57.816 500 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.86 % Favored : 92.91 % Rotamer: Outliers : 2.47 % Allowed : 5.22 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.85 (0.40), residues: 424 helix: -3.32 (0.76), residues: 24 sheet: 0.44 (0.40), residues: 169 loop : -1.02 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 116 HIS 0.004 0.002 HIS H 35 PHE 0.014 0.002 PHE B 515 TYR 0.017 0.002 TYR B 495 ARG 0.004 0.001 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00050 ( 1) link_NAG-ASN : angle 1.69120 ( 3) hydrogen bonds : bond 0.04813 ( 102) hydrogen bonds : angle 5.79545 ( 255) SS BOND : bond 0.00539 ( 6) SS BOND : angle 1.55551 ( 12) covalent geometry : bond 0.00490 ( 3439) covalent geometry : angle 0.64735 ( 4670) *********************** 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 64 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.354 Fit side-chains REVERT: B 356 LYS cc_start: 0.8143 (ttmm) cc_final: 0.7916 (ttmm) REVERT: B 370 ASN cc_start: 0.7327 (m-40) cc_final: 0.6935 (m-40) REVERT: B 468 ILE cc_start: 0.8236 (pt) cc_final: 0.8004 (mm) outliers start: 7 outliers final: 2 residues processed: 59 average time/residue: 0.8535 time to fit residues: 52.4891 Evaluate side-chains 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.0020 chunk 17 optimal weight: 0.0060 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 0.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN B 506 GLN H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.149318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.131638 restraints weight = 9365.114| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.50 r_work: 0.3809 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3446 Z= 0.105 Angle : 0.541 5.225 4685 Z= 0.288 Chirality : 0.044 0.141 498 Planarity : 0.004 0.054 604 Dihedral : 5.543 55.473 500 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 2.20 % Allowed : 7.14 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.86 (0.40), residues: 424 helix: -3.44 (0.65), residues: 32 sheet: 0.60 (0.40), residues: 166 loop : -1.04 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.006 0.001 PHE B 515 TYR 0.009 0.001 TYR B 495 ARG 0.002 0.000 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 1) link_NAG-ASN : angle 1.45102 ( 3) hydrogen bonds : bond 0.03514 ( 102) hydrogen bonds : angle 5.40496 ( 255) SS BOND : bond 0.00319 ( 6) SS BOND : angle 0.94518 ( 12) covalent geometry : bond 0.00232 ( 3439) covalent geometry : angle 0.53851 ( 4670) *********************** 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 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.341 Fit side-chains REVERT: B 370 ASN cc_start: 0.7371 (m-40) cc_final: 0.7023 (m-40) REVERT: B 468 ILE cc_start: 0.8192 (pt) cc_final: 0.7966 (mm) outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 0.8327 time to fit residues: 47.9637 Evaluate side-chains 58 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.0570 chunk 32 optimal weight: 0.0570 chunk 30 optimal weight: 0.4980 chunk 39 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN B 506 GLN H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.149403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.133254 restraints weight = 6200.699| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.93 r_work: 0.3846 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3446 Z= 0.114 Angle : 0.549 6.725 4685 Z= 0.291 Chirality : 0.044 0.146 498 Planarity : 0.004 0.052 604 Dihedral : 5.526 55.573 500 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 2.20 % Allowed : 8.52 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.83 (0.40), residues: 424 helix: -3.55 (0.62), residues: 32 sheet: 0.67 (0.40), residues: 166 loop : -1.04 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE B 515 TYR 0.011 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00042 ( 1) link_NAG-ASN : angle 1.47529 ( 3) hydrogen bonds : bond 0.03499 ( 102) hydrogen bonds : angle 5.27165 ( 255) SS BOND : bond 0.00358 ( 6) SS BOND : angle 0.98633 ( 12) covalent geometry : bond 0.00257 ( 3439) covalent geometry : angle 0.54589 ( 4670) *********************** 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 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.366 Fit side-chains REVERT: B 370 ASN cc_start: 0.7326 (m-40) cc_final: 0.7029 (m-40) outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 0.8303 time to fit residues: 48.6362 Evaluate side-chains 55 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 17 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.147796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.132915 restraints weight = 4330.377| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.56 r_work: 0.3850 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3446 Z= 0.179 Angle : 0.629 8.002 4685 Z= 0.332 Chirality : 0.047 0.169 498 Planarity : 0.005 0.053 604 Dihedral : 5.871 57.317 500 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 2.75 % Allowed : 8.24 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.83 (0.40), residues: 424 helix: -3.58 (0.69), residues: 25 sheet: 0.51 (0.40), residues: 168 loop : -1.00 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 116 HIS 0.004 0.002 HIS H 35 PHE 0.011 0.001 PHE B 515 TYR 0.016 0.002 TYR B 495 ARG 0.003 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 1) link_NAG-ASN : angle 1.74040 ( 3) hydrogen bonds : bond 0.04263 ( 102) hydrogen bonds : angle 5.47754 ( 255) SS BOND : bond 0.00445 ( 6) SS BOND : angle 1.87276 ( 12) covalent geometry : bond 0.00425 ( 3439) covalent geometry : angle 0.62170 ( 4670) *********************** 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 59 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.325 Fit side-chains REVERT: B 370 ASN cc_start: 0.7301 (m-40) cc_final: 0.6964 (m-40) REVERT: B 468 ILE cc_start: 0.8165 (pt) cc_final: 0.7956 (mm) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.8728 time to fit residues: 47.3479 Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.0040 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 overall best weight: 0.2970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.148734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.129741 restraints weight = 12100.696| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.90 r_work: 0.3757 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3446 Z= 0.134 Angle : 0.586 7.442 4685 Z= 0.306 Chirality : 0.045 0.155 498 Planarity : 0.004 0.052 604 Dihedral : 5.690 56.238 500 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 2.47 % Allowed : 9.34 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.79 (0.40), residues: 424 helix: -3.56 (0.70), residues: 25 sheet: 0.50 (0.40), residues: 168 loop : -0.94 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.008 0.001 PHE B 515 TYR 0.012 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00003 ( 1) link_NAG-ASN : angle 1.61244 ( 3) hydrogen bonds : bond 0.03751 ( 102) hydrogen bonds : angle 5.36078 ( 255) SS BOND : bond 0.00349 ( 6) SS BOND : angle 1.35261 ( 12) covalent geometry : bond 0.00311 ( 3439) covalent geometry : angle 0.58116 ( 4670) *********************** 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 61 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.359 Fit side-chains REVERT: B 370 ASN cc_start: 0.7319 (m-40) cc_final: 0.6970 (m-40) outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 0.8919 time to fit residues: 50.2416 Evaluate side-chains 59 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 35 optimal weight: 0.0030 overall best weight: 0.2368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.149286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.132649 restraints weight = 6550.386| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.01 r_work: 0.3831 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3446 Z= 0.118 Angle : 0.576 8.361 4685 Z= 0.297 Chirality : 0.045 0.138 498 Planarity : 0.004 0.051 604 Dihedral : 5.580 55.640 500 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 2.20 % Allowed : 10.44 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.74 (0.40), residues: 424 helix: -3.57 (0.68), residues: 25 sheet: 0.55 (0.40), residues: 168 loop : -0.92 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE B 515 TYR 0.011 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00026 ( 1) link_NAG-ASN : angle 1.54227 ( 3) hydrogen bonds : bond 0.03500 ( 102) hydrogen bonds : angle 5.24732 ( 255) SS BOND : bond 0.00305 ( 6) SS BOND : angle 1.17060 ( 12) covalent geometry : bond 0.00269 ( 3439) covalent geometry : angle 0.57207 ( 4670) *********************** 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 59 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.426 Fit side-chains REVERT: B 370 ASN cc_start: 0.7349 (m-40) cc_final: 0.7057 (m-40) REVERT: B 468 ILE cc_start: 0.8187 (pt) cc_final: 0.7965 (mm) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.8699 time to fit residues: 49.0620 Evaluate side-chains 55 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.0570 chunk 8 optimal weight: 0.0010 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.0570 chunk 21 optimal weight: 0.2980 chunk 1 optimal weight: 0.3980 overall best weight: 0.1622 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.150547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.131354 restraints weight = 12485.814| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.98 r_work: 0.3781 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3446 Z= 0.098 Angle : 0.542 7.882 4685 Z= 0.281 Chirality : 0.044 0.131 498 Planarity : 0.004 0.051 604 Dihedral : 5.405 54.977 500 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 1.65 % Allowed : 10.99 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.69 (0.40), residues: 424 helix: -3.55 (0.70), residues: 24 sheet: 0.56 (0.40), residues: 168 loop : -0.88 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.006 0.001 PHE L 83 TYR 0.009 0.001 TYR B 495 ARG 0.001 0.000 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00047 ( 1) link_NAG-ASN : angle 1.42391 ( 3) hydrogen bonds : bond 0.03115 ( 102) hydrogen bonds : angle 5.06228 ( 255) SS BOND : bond 0.00286 ( 6) SS BOND : angle 1.02301 ( 12) covalent geometry : bond 0.00217 ( 3439) covalent geometry : angle 0.53889 ( 4670) *********************** 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 62 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.356 Fit side-chains REVERT: B 370 ASN cc_start: 0.7333 (m-40) cc_final: 0.7047 (m-40) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 0.8983 time to fit residues: 55.2097 Evaluate side-chains 58 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 58 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.0670 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 0.0470 chunk 24 optimal weight: 0.0870 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN H 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.149551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.129710 restraints weight = 14728.138| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.25 r_work: 0.3747 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3446 Z= 0.122 Angle : 0.586 9.500 4685 Z= 0.301 Chirality : 0.045 0.140 498 Planarity : 0.004 0.051 604 Dihedral : 5.543 55.691 500 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 2.20 % Allowed : 12.64 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.74 (0.40), residues: 424 helix: -3.54 (0.69), residues: 25 sheet: 0.52 (0.40), residues: 168 loop : -0.89 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.007 0.001 PHE B 515 TYR 0.012 0.001 TYR B 495 ARG 0.003 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00033 ( 1) link_NAG-ASN : angle 1.50138 ( 3) hydrogen bonds : bond 0.03444 ( 102) hydrogen bonds : angle 5.10607 ( 255) SS BOND : bond 0.00308 ( 6) SS BOND : angle 1.17666 ( 12) covalent geometry : bond 0.00282 ( 3439) covalent geometry : angle 0.58248 ( 4670) *********************** 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 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.358 Fit side-chains REVERT: B 370 ASN cc_start: 0.7345 (m-40) cc_final: 0.7020 (m-40) REVERT: B 468 ILE cc_start: 0.8155 (pt) cc_final: 0.7944 (mm) outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 0.9021 time to fit residues: 51.6887 Evaluate side-chains 58 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain L residue 9 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.0040 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 0.0770 chunk 18 optimal weight: 0.8980 chunk 31 optimal weight: 0.0770 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 0.0870 overall best weight: 0.1286 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.151427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.133289 restraints weight = 9363.220| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.50 r_work: 0.3826 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3446 Z= 0.097 Angle : 0.557 9.608 4685 Z= 0.286 Chirality : 0.044 0.126 498 Planarity : 0.004 0.051 604 Dihedral : 5.330 54.621 500 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 2.20 % Allowed : 12.91 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.63 (0.41), residues: 424 helix: -3.57 (0.85), residues: 18 sheet: 0.56 (0.40), residues: 168 loop : -0.88 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.005 0.001 PHE L 83 TYR 0.008 0.001 TYR B 495 ARG 0.001 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 1.36494 ( 3) hydrogen bonds : bond 0.02949 ( 102) hydrogen bonds : angle 4.96276 ( 255) SS BOND : bond 0.00232 ( 6) SS BOND : angle 0.94353 ( 12) covalent geometry : bond 0.00218 ( 3439) covalent geometry : angle 0.55470 ( 4670) ********************** 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 62 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.295 Fit side-chains REVERT: B 370 ASN cc_start: 0.7368 (m-40) cc_final: 0.7130 (m-40) outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 0.7590 time to fit residues: 45.3719 Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain L residue 9 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.0170 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 40 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.147588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.131525 restraints weight = 6248.511| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.91 r_work: 0.3817 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3446 Z= 0.185 Angle : 0.668 11.136 4685 Z= 0.341 Chirality : 0.047 0.161 498 Planarity : 0.005 0.050 604 Dihedral : 5.845 57.151 500 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 1.92 % Allowed : 12.91 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.40), residues: 424 helix: -3.46 (0.73), residues: 25 sheet: 0.37 (0.40), residues: 163 loop : -0.95 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 116 HIS 0.005 0.002 HIS H 35 PHE 0.010 0.001 PHE B 515 TYR 0.017 0.002 TYR B 495 ARG 0.004 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 1) link_NAG-ASN : angle 1.73027 ( 3) hydrogen bonds : bond 0.04148 ( 102) hydrogen bonds : angle 5.29531 ( 255) SS BOND : bond 0.00427 ( 6) SS BOND : angle 1.55906 ( 12) covalent geometry : bond 0.00442 ( 3439) covalent geometry : angle 0.66313 ( 4670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4513.34 seconds wall clock time: 77 minutes 33.62 seconds (4653.62 seconds total)