Starting phenix.real_space_refine on Sat May 10 06:11:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsi_38619/05_2025/8xsi_38619.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsi_38619/05_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_38619/05_2025/8xsi_38619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsi_38619/05_2025/8xsi_38619.map" model { file = "/net/cci-nas-00/data/ceres_data/8xsi_38619/05_2025/8xsi_38619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsi_38619/05_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-5687/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: 3.49, per 1000 atoms: 1.04 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: 0.81 Conformation dependent library (CDL) restraints added in 574.8 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: 0.39 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: 0.80 Time building geometry restraints manager: 0.96 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.460 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:10.780 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- 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 : 0.359 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: 0.7995 time to fit residues: 46.8868 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 : 0.317 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.129367 restraints weight = 9052.285| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.46 r_work: 0.3771 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.70 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 = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- 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 : 0.317 Fit side-chains REVERT: B 356 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7913 (ttmm) REVERT: B 370 ASN cc_start: 0.7330 (m-40) cc_final: 0.6937 (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: 0.8447 time to fit residues: 51.9834 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 : 0.312 ------------------------------------------------------------------------------- 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: 0.0980 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.1986 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.149401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.131695 restraints weight = 9351.770| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.49 r_work: 0.3808 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3446 Z= 0.108 Angle : 0.542 5.273 4685 Z= 0.289 Chirality : 0.044 0.141 498 Planarity : 0.004 0.054 604 Dihedral : 5.539 55.361 500 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 0.007 0.001 PHE B 515 TYR 0.010 0.001 TYR B 495 ARG 0.002 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00030 ( 1) link_NAG-ASN : angle 1.46755 ( 3) hydrogen bonds : bond 0.03510 ( 102) hydrogen bonds : angle 5.38902 ( 255) SS BOND : bond 0.00334 ( 6) SS BOND : angle 0.96164 ( 12) covalent geometry : bond 0.00239 ( 3439) covalent geometry : angle 0.53924 ( 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 : 0.310 Fit side-chains REVERT: B 370 ASN cc_start: 0.7371 (m-40) cc_final: 0.7029 (m-40) outliers start: 6 outliers final: 5 residues processed: 55 average time/residue: 0.7654 time to fit residues: 44.1421 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 : 0.375 ------------------------------------------------------------------------------- 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: 0.1980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 overall best weight: 0.2478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.149043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.132907 restraints weight = 6192.500| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.92 r_work: 0.3842 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1125 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= 0.121 Angle : 0.555 6.517 4685 Z= 0.296 Chirality : 0.044 0.150 498 Planarity : 0.004 0.053 604 Dihedral : 5.576 55.806 500 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 2.75 % Allowed : 8.52 % Favored : 88.74 % 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: -3.54 (0.62), residues: 32 sheet: 0.65 (0.40), residues: 166 loop : -1.06 (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 0.012 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00037 ( 1) link_NAG-ASN : angle 1.50601 ( 3) hydrogen bonds : bond 0.03622 ( 102) hydrogen bonds : angle 5.31070 ( 255) SS BOND : bond 0.00362 ( 6) SS BOND : angle 1.03737 ( 12) covalent geometry : bond 0.00279 ( 3439) covalent geometry : angle 0.55234 ( 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 66 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.339 Fit side-chains REVERT: B 370 ASN cc_start: 0.7332 (m-40) cc_final: 0.7026 (m-40) REVERT: B 468 ILE cc_start: 0.8159 (pt) cc_final: 0.7955 (mm) outliers start: 8 outliers final: 2 residues processed: 61 average time/residue: 0.8323 time to fit residues: 53.0447 Evaluate side-chains 59 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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: 0.1980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 0.0770 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.148453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.133629 restraints weight = 4342.378| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.56 r_work: 0.3862 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3446 Z= 0.140 Angle : 0.580 6.794 4685 Z= 0.307 Chirality : 0.045 0.156 498 Planarity : 0.004 0.052 604 Dihedral : 5.668 56.366 500 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 2.47 % Allowed : 9.07 % Favored : 88.46 % 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: -0.77 (0.40), residues: 424 helix: -3.53 (0.72), residues: 24 sheet: 0.54 (0.40), residues: 168 loop : -0.97 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.009 0.001 PHE B 515 TYR 0.013 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00009 ( 1) link_NAG-ASN : angle 1.61143 ( 3) hydrogen bonds : bond 0.03810 ( 102) hydrogen bonds : angle 5.34477 ( 255) SS BOND : bond 0.00368 ( 6) SS BOND : angle 1.60991 ( 12) covalent geometry : bond 0.00329 ( 3439) covalent geometry : angle 0.57402 ( 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 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.330 Fit side-chains REVERT: B 370 ASN cc_start: 0.7310 (m-40) cc_final: 0.7014 (m-40) REVERT: B 468 ILE cc_start: 0.8148 (pt) cc_final: 0.7943 (mm) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.8535 time to fit residues: 48.1002 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 : 0.323 ------------------------------------------------------------------------------- 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 19 ARG 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: 0.8980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 0.0170 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 0.0970 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 GLN H 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.148691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.129775 restraints weight = 12099.035| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.91 r_work: 0.3760 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1240 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= 0.130 Angle : 0.568 7.267 4685 Z= 0.300 Chirality : 0.045 0.153 498 Planarity : 0.004 0.052 604 Dihedral : 5.627 56.057 500 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 2.75 % Allowed : 9.34 % Favored : 87.91 % 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: -0.77 (0.40), residues: 424 helix: -3.54 (0.70), residues: 25 sheet: 0.56 (0.40), residues: 168 loop : -0.97 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 0.00002 ( 1) link_NAG-ASN : angle 1.58327 ( 3) hydrogen bonds : bond 0.03684 ( 102) hydrogen bonds : angle 5.32194 ( 255) SS BOND : bond 0.00337 ( 6) SS BOND : angle 1.33849 ( 12) covalent geometry : bond 0.00303 ( 3439) covalent geometry : angle 0.56356 ( 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 62 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.319 Fit side-chains REVERT: B 370 ASN cc_start: 0.7317 (m-40) cc_final: 0.7004 (m-40) REVERT: B 468 ILE cc_start: 0.8146 (pt) cc_final: 0.7945 (mm) outliers start: 8 outliers final: 4 residues processed: 55 average time/residue: 0.8086 time to fit residues: 46.4450 Evaluate side-chains 58 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 5 optimal weight: 0.1980 chunk 11 optimal weight: 0.0020 chunk 13 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 overall best weight: 0.1186 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.150947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.134617 restraints weight = 6618.204| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.01 r_work: 0.3868 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1386 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= 0.089 Angle : 0.509 7.270 4685 Z= 0.270 Chirality : 0.043 0.126 498 Planarity : 0.004 0.051 604 Dihedral : 5.291 54.438 500 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 2.20 % Allowed : 9.89 % Favored : 87.91 % 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: -0.73 (0.40), residues: 424 helix: -3.46 (0.75), residues: 26 sheet: 0.70 (0.40), residues: 166 loop : -1.03 (0.40), residues: 232 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 L 83 TYR 0.008 0.001 TYR B 495 ARG 0.001 0.000 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00080 ( 1) link_NAG-ASN : angle 1.34408 ( 3) hydrogen bonds : bond 0.02962 ( 102) hydrogen bonds : angle 5.06702 ( 255) SS BOND : bond 0.00267 ( 6) SS BOND : angle 0.99814 ( 12) covalent geometry : bond 0.00194 ( 3439) covalent geometry : angle 0.50665 ( 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 67 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.326 Fit side-chains REVERT: B 370 ASN cc_start: 0.7344 (m-40) cc_final: 0.7094 (m-40) outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 0.8176 time to fit residues: 52.8416 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 : 0.322 ------------------------------------------------------------------------------- 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 10 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.0470 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.148293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.129199 restraints weight = 12445.929| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.94 r_work: 0.3751 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3446 Z= 0.159 Angle : 0.617 9.034 4685 Z= 0.323 Chirality : 0.046 0.159 498 Planarity : 0.005 0.052 604 Dihedral : 5.742 56.818 500 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 2.20 % Allowed : 10.99 % Favored : 86.81 % 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: -0.76 (0.40), residues: 424 helix: -3.49 (0.72), residues: 25 sheet: 0.59 (0.40), residues: 168 loop : -0.99 (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 0.009 0.001 PHE B 515 TYR 0.016 0.002 TYR B 495 ARG 0.003 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00042 ( 1) link_NAG-ASN : angle 1.67232 ( 3) hydrogen bonds : bond 0.03972 ( 102) hydrogen bonds : angle 5.29539 ( 255) SS BOND : bond 0.00405 ( 6) SS BOND : angle 1.41761 ( 12) covalent geometry : bond 0.00377 ( 3439) covalent geometry : angle 0.61219 ( 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 59 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.356 Fit side-chains REVERT: B 370 ASN cc_start: 0.7326 (m-40) cc_final: 0.6991 (m-40) REVERT: B 468 ILE cc_start: 0.8165 (pt) cc_final: 0.7965 (mm) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.8073 time to fit residues: 45.5908 Evaluate side-chains 57 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 L residue 10 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 24 optimal weight: 0.0970 chunk 7 optimal weight: 0.0170 chunk 14 optimal weight: 0.2980 overall best weight: 0.2416 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.149596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.129704 restraints weight = 14771.055| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.28 r_work: 0.3748 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3446 Z= 0.121 Angle : 0.581 9.774 4685 Z= 0.301 Chirality : 0.045 0.148 498 Planarity : 0.004 0.051 604 Dihedral : 5.562 55.734 500 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 1.92 % Allowed : 11.54 % Favored : 86.54 % 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: -0.75 (0.40), residues: 424 helix: -3.49 (0.70), residues: 25 sheet: 0.57 (0.39), residues: 168 loop : -0.96 (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 H 110 ARG 0.002 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00013 ( 1) link_NAG-ASN : angle 1.53393 ( 3) hydrogen bonds : bond 0.03476 ( 102) hydrogen bonds : angle 5.18569 ( 255) SS BOND : bond 0.00299 ( 6) SS BOND : angle 1.15928 ( 12) covalent geometry : bond 0.00282 ( 3439) covalent geometry : angle 0.57783 ( 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 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 Fit side-chains REVERT: B 370 ASN cc_start: 0.7345 (m-40) cc_final: 0.7016 (m-40) REVERT: B 468 ILE cc_start: 0.8179 (pt) cc_final: 0.7972 (mm) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.8744 time to fit residues: 48.3640 Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 0.0770 chunk 15 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.2738 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.149155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.131134 restraints weight = 9341.226| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.49 r_work: 0.3791 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3446 Z= 0.132 Angle : 0.608 10.843 4685 Z= 0.313 Chirality : 0.045 0.152 498 Planarity : 0.004 0.050 604 Dihedral : 5.620 55.969 500 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 1.65 % Allowed : 12.91 % Favored : 85.44 % 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: -0.77 (0.40), residues: 424 helix: -3.50 (0.70), residues: 25 sheet: 0.57 (0.39), residues: 168 loop : -0.98 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.007 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 0.00008 ( 1) link_NAG-ASN : angle 1.55817 ( 3) hydrogen bonds : bond 0.03618 ( 102) hydrogen bonds : angle 5.19255 ( 255) SS BOND : bond 0.00329 ( 6) SS BOND : angle 1.24870 ( 12) covalent geometry : bond 0.00311 ( 3439) covalent geometry : angle 0.60390 ( 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 58 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.321 Fit side-chains REVERT: B 370 ASN cc_start: 0.7391 (m-40) cc_final: 0.7086 (m-40) REVERT: B 468 ILE cc_start: 0.8257 (pt) cc_final: 0.8028 (mm) outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.8465 time to fit residues: 47.7024 Evaluate side-chains 57 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.145522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.129565 restraints weight = 6215.792| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.91 r_work: 0.3789 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 3446 Z= 0.281 Angle : 0.754 12.721 4685 Z= 0.390 Chirality : 0.051 0.193 498 Planarity : 0.005 0.049 604 Dihedral : 6.274 58.975 500 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.62 % Favored : 93.14 % Rotamer: Outliers : 1.65 % Allowed : 12.64 % Favored : 85.71 % 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: -0.99 (0.39), residues: 424 helix: -3.49 (0.72), residues: 25 sheet: 0.47 (0.40), residues: 162 loop : -1.16 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP H 116 HIS 0.006 0.003 HIS H 35 PHE 0.015 0.002 PHE B 515 TYR 0.024 0.003 TYR H 110 ARG 0.005 0.001 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 1) link_NAG-ASN : angle 2.00053 ( 3) hydrogen bonds : bond 0.04985 ( 102) hydrogen bonds : angle 5.64648 ( 255) SS BOND : bond 0.00556 ( 6) SS BOND : angle 1.95018 ( 12) covalent geometry : bond 0.00682 ( 3439) covalent geometry : angle 0.74662 ( 4670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4218.16 seconds wall clock time: 72 minutes 54.55 seconds (4374.55 seconds total)