Starting phenix.real_space_refine on Fri Oct 10 12:45:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xsi_38619/10_2025/8xsi_38619.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xsi_38619/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xsi_38619/10_2025/8xsi_38619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xsi_38619/10_2025/8xsi_38619.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xsi_38619/10_2025/8xsi_38619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xsi_38619/10_2025/8xsi_38619.map" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.19, per 1000 atoms: 0.35 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: 0.22 Conformation dependent library (CDL) restraints added in 205.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.14 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: 0.48 Time building geometry restraints manager: 0.32 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.340 Find NCS groups from input model: 0.020 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG H 87 TYR 0.015 0.001 TYR B 495 PHE 0.008 0.001 PHE B 486 TRP 0.010 0.001 TRP H 116 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3439) covalent geometry : angle 0.60428 ( 4670) SS BOND : bond 0.00464 ( 6) SS BOND : angle 1.92695 ( 12) hydrogen bonds : bond 0.16616 ( 102) hydrogen bonds : angle 7.52024 ( 255) link_NAG-ASN : bond 0.00045 ( 1) link_NAG-ASN : angle 1.60260 ( 3) *********************** 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 : 0.126 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: 0.4153 time to fit residues: 24.2321 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 : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.0970 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 overall best weight: 0.2578 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.149195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.130516 restraints weight = 11525.558| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.85 r_work: 0.3780 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3779 r_free = 0.3779 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3446 Z= 0.126 Angle : 0.565 5.545 4685 Z= 0.303 Chirality : 0.045 0.153 498 Planarity : 0.005 0.054 604 Dihedral : 5.631 56.205 500 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 : 2.20 % Allowed : 5.77 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.40), residues: 424 helix: -3.40 (0.64), residues: 32 sheet: 0.61 (0.40), residues: 166 loop : -1.03 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.011 0.001 TYR B 495 PHE 0.008 0.001 PHE B 515 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3439) covalent geometry : angle 0.56222 ( 4670) SS BOND : bond 0.00400 ( 6) SS BOND : angle 1.16509 ( 12) hydrogen bonds : bond 0.03901 ( 102) hydrogen bonds : angle 5.60925 ( 255) link_NAG-ASN : bond 0.00094 ( 1) link_NAG-ASN : angle 1.38470 ( 3) *********************** 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 62 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.124 Fit side-chains REVERT: B 370 ASN cc_start: 0.7306 (m-40) cc_final: 0.6951 (m-40) outliers start: 6 outliers final: 3 residues processed: 56 average time/residue: 0.3871 time to fit residues: 22.5898 Evaluate side-chains 59 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 28 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 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.0770 chunk 30 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B 487 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.147970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.131643 restraints weight = 6214.259| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.94 r_work: 0.3822 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3446 Z= 0.165 Angle : 0.609 6.208 4685 Z= 0.324 Chirality : 0.046 0.165 498 Planarity : 0.005 0.054 604 Dihedral : 5.818 56.948 500 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 2.20 % Allowed : 7.42 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.40), residues: 424 helix: -3.46 (0.64), residues: 32 sheet: 0.60 (0.40), residues: 166 loop : -1.09 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.015 0.002 TYR B 495 PHE 0.011 0.001 PHE B 515 TRP 0.010 0.002 TRP H 47 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 3439) covalent geometry : angle 0.60515 ( 4670) SS BOND : bond 0.00449 ( 6) SS BOND : angle 1.27297 ( 12) hydrogen bonds : bond 0.04241 ( 102) hydrogen bonds : angle 5.53253 ( 255) link_NAG-ASN : bond 0.00018 ( 1) link_NAG-ASN : angle 1.67931 ( 3) *********************** 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 61 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.091 Fit side-chains REVERT: B 370 ASN cc_start: 0.7308 (m-40) cc_final: 0.6962 (m-40) REVERT: B 468 ILE cc_start: 0.8186 (pt) cc_final: 0.7970 (mm) outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 0.4164 time to fit residues: 24.2824 Evaluate side-chains 57 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain H residue 19 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 0.0870 chunk 24 optimal weight: 0.2980 chunk 7 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 5 optimal weight: 0.0040 chunk 29 optimal weight: 0.0670 overall best weight: 0.1308 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.150453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.133463 restraints weight = 7703.421| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.21 r_work: 0.3845 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3446 Z= 0.091 Angle : 0.512 5.440 4685 Z= 0.274 Chirality : 0.043 0.132 498 Planarity : 0.004 0.051 604 Dihedral : 5.401 54.977 500 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 3.02 % Allowed : 8.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.40), residues: 424 helix: -3.24 (0.77), residues: 26 sheet: 0.63 (0.40), residues: 167 loop : -1.04 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.008 0.001 TYR B 495 PHE 0.005 0.001 PHE B 515 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 3439) covalent geometry : angle 0.50981 ( 4670) SS BOND : bond 0.00271 ( 6) SS BOND : angle 0.82514 ( 12) hydrogen bonds : bond 0.03101 ( 102) hydrogen bonds : angle 5.21075 ( 255) link_NAG-ASN : bond 0.00089 ( 1) link_NAG-ASN : angle 1.37018 ( 3) *********************** 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 64 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.129 Fit side-chains REVERT: B 370 ASN cc_start: 0.7353 (m-40) cc_final: 0.7051 (m-40) REVERT: B 468 ILE cc_start: 0.8168 (pt) cc_final: 0.7958 (mm) outliers start: 9 outliers final: 4 residues processed: 57 average time/residue: 0.4098 time to fit residues: 24.3352 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 : 0.129 ------------------------------------------------------------------------------- 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 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 7 optimal weight: 0.0670 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.0870 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.148936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.134285 restraints weight = 4247.397| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.54 r_work: 0.3878 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1137 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= 0.132 Angle : 0.572 6.437 4685 Z= 0.303 Chirality : 0.045 0.154 498 Planarity : 0.004 0.052 604 Dihedral : 5.582 56.038 500 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 2.47 % Allowed : 9.89 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.40), residues: 424 helix: -3.44 (0.64), residues: 32 sheet: 0.65 (0.40), residues: 166 loop : -1.02 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.014 0.001 TYR B 495 PHE 0.008 0.001 PHE B 515 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3439) covalent geometry : angle 0.56447 ( 4670) SS BOND : bond 0.00367 ( 6) SS BOND : angle 1.71075 ( 12) hydrogen bonds : bond 0.03694 ( 102) hydrogen bonds : angle 5.25229 ( 255) link_NAG-ASN : bond 0.00015 ( 1) link_NAG-ASN : angle 1.57341 ( 3) *********************** 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 62 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.125 Fit side-chains REVERT: B 370 ASN cc_start: 0.7303 (m-40) cc_final: 0.7038 (m-40) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.3922 time to fit residues: 22.8848 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 : 0.130 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 2 optimal weight: 0.1980 chunk 14 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.147535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.129283 restraints weight = 11318.128| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.72 r_work: 0.3758 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- 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 = 0.37 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1263 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= 0.172 Angle : 0.621 7.091 4685 Z= 0.328 Chirality : 0.047 0.169 498 Planarity : 0.005 0.053 604 Dihedral : 5.852 57.252 500 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.74 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.40), residues: 424 helix: -3.44 (0.72), residues: 25 sheet: 0.48 (0.40), residues: 169 loop : -0.96 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 403 TYR 0.015 0.002 TYR B 495 PHE 0.010 0.001 PHE B 515 TRP 0.011 0.002 TRP H 47 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 3439) covalent geometry : angle 0.61561 ( 4670) SS BOND : bond 0.00435 ( 6) SS BOND : angle 1.54987 ( 12) hydrogen bonds : bond 0.04098 ( 102) hydrogen bonds : angle 5.44985 ( 255) link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 1.73182 ( 3) *********************** 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 58 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.123 Fit side-chains REVERT: B 370 ASN cc_start: 0.7308 (m-40) cc_final: 0.6969 (m-40) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.4321 time to fit residues: 23.3832 Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 35 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 0.0770 chunk 1 optimal weight: 0.3980 chunk 25 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 overall best weight: 0.1738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.149758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.131162 restraints weight = 11513.803| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.80 r_work: 0.3783 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3446 Z= 0.102 Angle : 0.544 7.090 4685 Z= 0.288 Chirality : 0.044 0.140 498 Planarity : 0.004 0.051 604 Dihedral : 5.506 55.383 500 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 2.20 % Allowed : 11.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.40), residues: 424 helix: -3.44 (0.70), residues: 25 sheet: 0.58 (0.40), residues: 168 loop : -0.89 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 403 TYR 0.008 0.001 TYR B 495 PHE 0.006 0.001 PHE L 83 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 3439) covalent geometry : angle 0.54080 ( 4670) SS BOND : bond 0.00283 ( 6) SS BOND : angle 1.06751 ( 12) hydrogen bonds : bond 0.03284 ( 102) hydrogen bonds : angle 5.20449 ( 255) link_NAG-ASN : bond 0.00038 ( 1) link_NAG-ASN : angle 1.47886 ( 3) *********************** 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 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.123 Fit side-chains REVERT: B 370 ASN cc_start: 0.7318 (m-40) cc_final: 0.7025 (m-40) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.4404 time to fit residues: 24.7417 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 : 0.127 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.0470 chunk 2 optimal weight: 0.0970 chunk 24 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 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 = 0.4110 r_free = 0.4110 target = 0.148210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.130907 restraints weight = 7913.112| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.24 r_work: 0.3800 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.38 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 = 0.40 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 = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3446 Z= 0.157 Angle : 0.608 8.315 4685 Z= 0.320 Chirality : 0.046 0.161 498 Planarity : 0.005 0.050 604 Dihedral : 5.766 56.832 500 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 1.92 % Allowed : 10.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.40), residues: 424 helix: -3.48 (0.71), residues: 25 sheet: 0.48 (0.40), residues: 169 loop : -0.95 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 403 TYR 0.014 0.002 TYR B 495 PHE 0.009 0.001 PHE B 515 TRP 0.011 0.002 TRP H 47 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3439) covalent geometry : angle 0.60331 ( 4670) SS BOND : bond 0.00391 ( 6) SS BOND : angle 1.32161 ( 12) hydrogen bonds : bond 0.03966 ( 102) hydrogen bonds : angle 5.33735 ( 255) link_NAG-ASN : bond 0.00027 ( 1) link_NAG-ASN : angle 1.68840 ( 3) *********************** 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 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.120 Fit side-chains REVERT: B 370 ASN cc_start: 0.7361 (m-40) cc_final: 0.7036 (m-40) outliers start: 5 outliers final: 5 residues processed: 55 average time/residue: 0.3977 time to fit residues: 22.8086 Evaluate side-chains 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.0670 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.147166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.128587 restraints weight = 11184.595| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.75 r_work: 0.3746 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- 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 = 0.43 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 = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 0.005 0.040 3446 Z= 0.198 Angle : 0.654 8.927 4685 Z= 0.344 Chirality : 0.047 0.176 498 Planarity : 0.005 0.051 604 Dihedral : 6.019 57.776 500 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 2.47 % Allowed : 10.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.40), residues: 424 helix: -3.44 (0.73), residues: 25 sheet: 0.47 (0.40), residues: 169 loop : -1.04 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.016 0.002 TYR H 110 PHE 0.011 0.002 PHE B 515 TRP 0.012 0.002 TRP H 116 HIS 0.005 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 3439) covalent geometry : angle 0.64883 ( 4670) SS BOND : bond 0.00436 ( 6) SS BOND : angle 1.49583 ( 12) hydrogen bonds : bond 0.04353 ( 102) hydrogen bonds : angle 5.48230 ( 255) link_NAG-ASN : bond 0.00061 ( 1) link_NAG-ASN : angle 1.83337 ( 3) *********************** 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 59 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.120 Fit side-chains REVERT: B 370 ASN cc_start: 0.7327 (m-40) cc_final: 0.6970 (m-40) outliers start: 7 outliers final: 5 residues processed: 53 average time/residue: 0.4436 time to fit residues: 24.3962 Evaluate side-chains 57 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.074 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.0170 chunk 36 optimal weight: 0.0980 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.148068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.129476 restraints weight = 11366.206| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.78 r_work: 0.3757 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1388 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= 0.156 Angle : 0.621 10.308 4685 Z= 0.325 Chirality : 0.046 0.163 498 Planarity : 0.005 0.052 604 Dihedral : 5.867 56.964 500 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 2.75 % Allowed : 10.99 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.40), residues: 424 helix: -3.46 (0.71), residues: 25 sheet: 0.43 (0.40), residues: 163 loop : -1.02 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.014 0.002 TYR H 110 PHE 0.009 0.001 PHE B 515 TRP 0.012 0.002 TRP H 47 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 3439) covalent geometry : angle 0.61704 ( 4670) SS BOND : bond 0.00362 ( 6) SS BOND : angle 1.33513 ( 12) hydrogen bonds : bond 0.03948 ( 102) hydrogen bonds : angle 5.37768 ( 255) link_NAG-ASN : bond 0.00034 ( 1) link_NAG-ASN : angle 1.72924 ( 3) ********************** 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: 8 poor density : 54 time to evaluate : 0.121 Fit side-chains REVERT: B 370 ASN cc_start: 0.7327 (m-40) cc_final: 0.6977 (m-40) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.4225 time to fit residues: 24.1510 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 : 0.135 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 0.0370 chunk 1 optimal weight: 0.0030 chunk 36 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 0.0050 chunk 16 optimal weight: 0.0000 overall best weight: 0.0886 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.151180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.133222 restraints weight = 10441.228| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.63 r_work: 0.3824 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3446 Z= 0.089 Angle : 0.538 10.125 4685 Z= 0.278 Chirality : 0.044 0.128 498 Planarity : 0.004 0.052 604 Dihedral : 5.353 54.213 500 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 2.47 % Allowed : 10.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.41), residues: 424 helix: -3.12 (1.22), residues: 12 sheet: 0.51 (0.40), residues: 169 loop : -0.97 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.007 0.001 TYR B 495 PHE 0.005 0.001 PHE L 98 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 3439) covalent geometry : angle 0.53564 ( 4670) SS BOND : bond 0.00212 ( 6) SS BOND : angle 0.91426 ( 12) hydrogen bonds : bond 0.02847 ( 102) hydrogen bonds : angle 5.03219 ( 255) link_NAG-ASN : bond 0.00055 ( 1) link_NAG-ASN : angle 1.36441 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2134.59 seconds wall clock time: 36 minutes 58.66 seconds (2218.66 seconds total)