Starting phenix.real_space_refine on Tue Mar 3 12:06:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mkm_23899/03_2026/7mkm_23899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mkm_23899/03_2026/7mkm_23899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mkm_23899/03_2026/7mkm_23899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mkm_23899/03_2026/7mkm_23899.map" model { file = "/net/cci-nas-00/data/ceres_data/7mkm_23899/03_2026/7mkm_23899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mkm_23899/03_2026/7mkm_23899.cif" } resolution = 3.16 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= 0.001 sd= 0.017 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 751 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 2030 2.51 5 N 528 2.21 5 O 617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3192 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1500 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 178} Chain: "H" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.74, per 1000 atoms: 0.23 Number of scatterers: 3192 At special positions: 0 Unit cell: (77.72, 67.28, 98.6, 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 617 8.00 N 528 7.00 C 2030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " 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 A 601 " - " ASN A 343 " Time building additional restraints: 0.17 Conformation dependent library (CDL) restraints added in 96.5 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 11.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'L' and resid 48 through 52 removed outlier: 3.810A pdb=" N ASN L 52 " --> pdb=" O ASP L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 4.100A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.734A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 46 through 48 removed outlier: 3.607A pdb=" N GLY H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 37 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN H 39 " --> pdb=" O LYS H 92 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS H 92 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 105 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 3 through 5 removed outlier: 3.771A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE L 74 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET L 21 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU L 72 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS L 23 " --> pdb=" O TYR L 70 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR L 71 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 47 removed outlier: 4.688A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN L 88 " --> pdb=" O TYR L 33 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR L 35 " --> pdb=" O TYR L 86 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 198 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: 0.38 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1009 1.34 - 1.46: 881 1.46 - 1.58: 1364 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3276 Sorted by residual: bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.426 -0.020 2.00e-02 2.50e+03 1.05e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.65e-01 bond pdb=" CA MET L 77 " pdb=" CB MET L 77 " ideal model delta sigma weight residual 1.513 1.536 -0.023 2.59e-02 1.49e+03 7.75e-01 bond pdb=" C2 NAG A 601 " pdb=" N2 NAG A 601 " ideal model delta sigma weight residual 1.439 1.454 -0.015 2.00e-02 2.50e+03 5.78e-01 ... (remaining 3271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 4317 2.13 - 4.25: 132 4.25 - 6.38: 4 6.38 - 8.50: 2 8.50 - 10.63: 2 Bond angle restraints: 4457 Sorted by residual: angle pdb=" C ARG L 76 " pdb=" N MET L 77 " pdb=" CA MET L 77 " ideal model delta sigma weight residual 122.04 130.76 -8.72 2.11e+00 2.25e-01 1.71e+01 angle pdb=" CA ARG L 60 " pdb=" CB ARG L 60 " pdb=" CG ARG L 60 " ideal model delta sigma weight residual 114.10 121.10 -7.00 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA LEU H 29 " pdb=" CB LEU H 29 " pdb=" CG LEU H 29 " ideal model delta sigma weight residual 116.30 126.93 -10.63 3.50e+00 8.16e-02 9.23e+00 angle pdb=" C LEU H 67 " pdb=" N SER H 68 " pdb=" CA SER H 68 " ideal model delta sigma weight residual 121.62 126.42 -4.80 1.83e+00 2.99e-01 6.87e+00 angle pdb=" C GLY L 65 " pdb=" N CYS L 66 " pdb=" CA CYS L 66 " ideal model delta sigma weight residual 122.59 126.34 -3.75 1.57e+00 4.06e-01 5.70e+00 ... (remaining 4452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 1753 17.71 - 35.41: 159 35.41 - 53.12: 21 53.12 - 70.82: 0 70.82 - 88.53: 2 Dihedral angle restraints: 1935 sinusoidal: 758 harmonic: 1177 Sorted by residual: dihedral pdb=" CA MET L 77 " pdb=" C MET L 77 " pdb=" N GLU L 78 " pdb=" CA GLU L 78 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR H 59 " pdb=" C TYR H 59 " pdb=" N ASN H 60 " pdb=" CA ASN H 60 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASP L 81 " pdb=" C ASP L 81 " pdb=" N ALA L 82 " pdb=" CA ALA L 82 " ideal model delta harmonic sigma weight residual -180.00 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 1932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 312 0.037 - 0.074: 113 0.074 - 0.111: 37 0.111 - 0.147: 16 0.147 - 0.184: 2 Chirality restraints: 480 Sorted by residual: chirality pdb=" CB ILE A 402 " pdb=" CA ILE A 402 " pdb=" CG1 ILE A 402 " pdb=" CG2 ILE A 402 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA ILE L 74 " pdb=" N ILE L 74 " pdb=" C ILE L 74 " pdb=" CB ILE L 74 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE L 47 " pdb=" N ILE L 47 " pdb=" C ILE L 47 " pdb=" CB ILE L 47 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 477 not shown) Planarity restraints: 573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO A 491 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.018 2.00e-02 2.50e+03 1.74e-02 3.80e+00 pdb=" CG ASN A 343 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 466 " -0.137 9.50e-02 1.11e+02 6.17e-02 2.96e+00 pdb=" NE ARG A 466 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 466 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 466 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 466 " -0.000 2.00e-02 2.50e+03 ... (remaining 570 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 130 2.72 - 3.27: 3159 3.27 - 3.81: 4603 3.81 - 4.36: 5272 4.36 - 4.90: 9289 Nonbonded interactions: 22453 Sorted by model distance: nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 21 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.274 3.040 nonbonded pdb=" O ASN A 440 " pdb=" ND2 ASN L 91 " model vdw 2.324 3.120 nonbonded pdb=" O ALA A 475 " pdb=" ND2 ASN A 487 " model vdw 2.382 3.120 nonbonded pdb=" OG1 THR A 393 " pdb=" O HIS A 519 " model vdw 2.394 3.040 ... (remaining 22448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.460 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 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 0.031 3282 Z= 0.131 Angle : 0.806 10.631 4470 Z= 0.434 Chirality : 0.047 0.184 480 Planarity : 0.006 0.062 572 Dihedral : 13.042 88.529 1176 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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 are not related in a simple way. whole: -1.30 (0.38), residues: 400 helix: -3.71 (0.45), residues: 32 sheet: 2.48 (0.49), residues: 100 loop : -2.02 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 466 TYR 0.018 0.003 TYR L 85 PHE 0.015 0.002 PHE A 429 TRP 0.022 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 3276) covalent geometry : angle 0.79467 ( 4457) SS BOND : bond 0.00488 ( 5) SS BOND : angle 1.19163 ( 10) hydrogen bonds : bond 0.30388 ( 72) hydrogen bonds : angle 12.10241 ( 198) link_NAG-ASN : bond 0.00004 ( 1) link_NAG-ASN : angle 5.05605 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.108 Fit side-chains REVERT: A 486 PHE cc_start: 0.6384 (t80) cc_final: 0.6143 (t80) REVERT: L 34 TRP cc_start: 0.4286 (m100) cc_final: 0.4080 (m100) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0615 time to fit residues: 4.5540 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.0270 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 37 optimal weight: 0.5980 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN L 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.201286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.178554 restraints weight = 5169.811| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 2.97 r_work: 0.4330 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3282 Z= 0.139 Angle : 0.714 8.119 4470 Z= 0.386 Chirality : 0.047 0.265 480 Planarity : 0.005 0.053 572 Dihedral : 7.522 26.127 471 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.15 % Allowed : 9.77 % Favored : 89.08 % 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 are not related in a simple way. whole: -1.07 (0.39), residues: 400 helix: -2.39 (0.85), residues: 26 sheet: 1.60 (0.46), residues: 115 loop : -1.77 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 60 TYR 0.026 0.002 TYR A 423 PHE 0.028 0.002 PHE A 400 TRP 0.019 0.002 TRP A 436 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3276) covalent geometry : angle 0.70857 ( 4457) SS BOND : bond 0.00529 ( 5) SS BOND : angle 1.17588 ( 10) hydrogen bonds : bond 0.04607 ( 72) hydrogen bonds : angle 8.93729 ( 198) link_NAG-ASN : bond 0.00496 ( 1) link_NAG-ASN : angle 2.89841 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.120 Fit side-chains REVERT: A 365 TYR cc_start: 0.6379 (m-80) cc_final: 0.5722 (m-80) REVERT: A 465 GLU cc_start: 0.6811 (tp30) cc_final: 0.6381 (tp30) REVERT: A 466 ARG cc_start: 0.8014 (mtm-85) cc_final: 0.7310 (mtm-85) REVERT: A 486 PHE cc_start: 0.7044 (t80) cc_final: 0.6549 (t80) REVERT: L 68 THR cc_start: 0.7278 (OUTLIER) cc_final: 0.7076 (m) REVERT: L 86 TYR cc_start: 0.5438 (m-10) cc_final: 0.5064 (m-10) outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 0.0752 time to fit residues: 5.2702 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 22 optimal weight: 0.0980 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.0470 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.199535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.176622 restraints weight = 5129.298| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 3.03 r_work: 0.4299 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3282 Z= 0.137 Angle : 0.676 8.433 4470 Z= 0.366 Chirality : 0.045 0.265 480 Planarity : 0.005 0.051 572 Dihedral : 6.900 27.354 471 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.30 % Allowed : 12.64 % Favored : 85.06 % 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 are not related in a simple way. whole: -1.23 (0.39), residues: 400 helix: -1.89 (1.02), residues: 27 sheet: 1.07 (0.44), residues: 115 loop : -1.71 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.012 0.002 TYR A 453 PHE 0.012 0.002 PHE A 400 TRP 0.024 0.002 TRP H 36 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 3276) covalent geometry : angle 0.67202 ( 4457) SS BOND : bond 0.00515 ( 5) SS BOND : angle 0.99735 ( 10) hydrogen bonds : bond 0.04624 ( 72) hydrogen bonds : angle 8.01872 ( 198) link_NAG-ASN : bond 0.00302 ( 1) link_NAG-ASN : angle 2.49800 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.112 Fit side-chains REVERT: A 365 TYR cc_start: 0.6451 (m-80) cc_final: 0.5767 (m-80) REVERT: A 465 GLU cc_start: 0.7144 (tp30) cc_final: 0.6757 (tp30) REVERT: A 486 PHE cc_start: 0.6999 (t80) cc_final: 0.6545 (t80) REVERT: L 68 THR cc_start: 0.6876 (OUTLIER) cc_final: 0.6625 (m) outliers start: 8 outliers final: 3 residues processed: 54 average time/residue: 0.0730 time to fit residues: 4.7784 Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.2980 chunk 13 optimal weight: 0.0040 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.195288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.174241 restraints weight = 5105.279| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.67 r_work: 0.4297 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3282 Z= 0.136 Angle : 0.658 8.363 4470 Z= 0.355 Chirality : 0.045 0.239 480 Planarity : 0.005 0.050 572 Dihedral : 6.578 27.339 471 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.01 % Allowed : 13.51 % Favored : 84.48 % 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 are not related in a simple way. whole: -1.44 (0.39), residues: 400 helix: -1.89 (1.01), residues: 27 sheet: 0.88 (0.46), residues: 108 loop : -1.78 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 355 TYR 0.020 0.002 TYR A 423 PHE 0.012 0.002 PHE A 400 TRP 0.024 0.003 TRP H 47 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3276) covalent geometry : angle 0.65404 ( 4457) SS BOND : bond 0.00512 ( 5) SS BOND : angle 1.02325 ( 10) hydrogen bonds : bond 0.04199 ( 72) hydrogen bonds : angle 7.67993 ( 198) link_NAG-ASN : bond 0.00282 ( 1) link_NAG-ASN : angle 2.38320 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.069 Fit side-chains REVERT: A 465 GLU cc_start: 0.7031 (tp30) cc_final: 0.6736 (tp30) REVERT: A 486 PHE cc_start: 0.6774 (t80) cc_final: 0.6432 (t80) outliers start: 7 outliers final: 2 residues processed: 55 average time/residue: 0.0671 time to fit residues: 4.5006 Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.0070 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.192780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.171619 restraints weight = 5201.775| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 2.73 r_work: 0.4269 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3282 Z= 0.156 Angle : 0.680 8.307 4470 Z= 0.369 Chirality : 0.045 0.236 480 Planarity : 0.005 0.052 572 Dihedral : 6.564 27.373 471 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.30 % Allowed : 14.37 % Favored : 83.33 % 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 are not related in a simple way. whole: -1.73 (0.39), residues: 400 helix: -2.00 (1.00), residues: 27 sheet: 0.38 (0.46), residues: 108 loop : -1.84 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 97 TYR 0.015 0.002 TYR H 58 PHE 0.010 0.002 PHE A 497 TRP 0.023 0.003 TRP H 36 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 3276) covalent geometry : angle 0.67533 ( 4457) SS BOND : bond 0.00521 ( 5) SS BOND : angle 1.05919 ( 10) hydrogen bonds : bond 0.04684 ( 72) hydrogen bonds : angle 7.59127 ( 198) link_NAG-ASN : bond 0.00255 ( 1) link_NAG-ASN : angle 2.62851 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.119 Fit side-chains REVERT: A 465 GLU cc_start: 0.7043 (tp30) cc_final: 0.6775 (tp30) REVERT: A 466 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7323 (mtm-85) REVERT: A 486 PHE cc_start: 0.6739 (t80) cc_final: 0.6455 (t80) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 0.0716 time to fit residues: 4.6253 Evaluate side-chains 50 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.0060 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.192111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.171127 restraints weight = 5102.612| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 2.69 r_work: 0.4266 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3282 Z= 0.153 Angle : 0.675 8.211 4470 Z= 0.364 Chirality : 0.044 0.204 480 Planarity : 0.005 0.049 572 Dihedral : 6.439 27.026 471 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.59 % Allowed : 14.66 % Favored : 82.76 % 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 are not related in a simple way. whole: -1.86 (0.39), residues: 400 helix: -1.95 (1.02), residues: 27 sheet: 0.32 (0.48), residues: 104 loop : -1.94 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 355 TYR 0.014 0.002 TYR H 58 PHE 0.010 0.002 PHE A 400 TRP 0.022 0.002 TRP H 36 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3276) covalent geometry : angle 0.67034 ( 4457) SS BOND : bond 0.00497 ( 5) SS BOND : angle 1.05157 ( 10) hydrogen bonds : bond 0.04463 ( 72) hydrogen bonds : angle 7.56478 ( 198) link_NAG-ASN : bond 0.00232 ( 1) link_NAG-ASN : angle 2.59884 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.108 Fit side-chains REVERT: A 465 GLU cc_start: 0.6984 (tp30) cc_final: 0.6759 (tp30) REVERT: A 466 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.7334 (mtm-85) REVERT: A 486 PHE cc_start: 0.6678 (t80) cc_final: 0.6398 (t80) REVERT: A 509 ARG cc_start: 0.6947 (mtt180) cc_final: 0.6004 (mtp85) outliers start: 9 outliers final: 7 residues processed: 53 average time/residue: 0.0856 time to fit residues: 5.3747 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.192531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.170994 restraints weight = 5200.334| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 2.87 r_work: 0.4255 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3282 Z= 0.147 Angle : 0.683 8.155 4470 Z= 0.366 Chirality : 0.044 0.191 480 Planarity : 0.005 0.049 572 Dihedral : 6.264 26.678 471 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.01 % Allowed : 15.52 % Favored : 82.47 % 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 are not related in a simple way. whole: -1.98 (0.39), residues: 400 helix: -1.92 (1.04), residues: 27 sheet: 0.30 (0.51), residues: 99 loop : -2.02 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 44 TYR 0.016 0.002 TYR L 35 PHE 0.011 0.002 PHE A 400 TRP 0.022 0.002 TRP H 36 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3276) covalent geometry : angle 0.67925 ( 4457) SS BOND : bond 0.00465 ( 5) SS BOND : angle 1.05410 ( 10) hydrogen bonds : bond 0.04281 ( 72) hydrogen bonds : angle 7.56790 ( 198) link_NAG-ASN : bond 0.00171 ( 1) link_NAG-ASN : angle 2.49433 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.107 Fit side-chains REVERT: A 466 ARG cc_start: 0.8045 (mtm-85) cc_final: 0.7360 (mtm-85) REVERT: A 486 PHE cc_start: 0.6701 (t80) cc_final: 0.6407 (t80) REVERT: A 509 ARG cc_start: 0.7002 (mtt180) cc_final: 0.6009 (mtp85) REVERT: H 103 ASP cc_start: 0.7645 (t0) cc_final: 0.7327 (m-30) outliers start: 7 outliers final: 7 residues processed: 53 average time/residue: 0.0829 time to fit residues: 5.2589 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.0170 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 23 optimal weight: 0.1980 overall best weight: 0.2618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.194154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.172583 restraints weight = 5183.441| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 2.87 r_work: 0.4276 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3282 Z= 0.120 Angle : 0.661 8.000 4470 Z= 0.352 Chirality : 0.044 0.158 480 Planarity : 0.004 0.046 572 Dihedral : 5.929 25.924 471 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.01 % Allowed : 15.52 % Favored : 82.47 % 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 are not related in a simple way. whole: -1.89 (0.40), residues: 400 helix: -1.81 (1.05), residues: 27 sheet: 0.15 (0.51), residues: 102 loop : -1.89 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 466 TYR 0.015 0.001 TYR L 35 PHE 0.012 0.001 PHE A 400 TRP 0.023 0.002 TRP H 36 HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 3276) covalent geometry : angle 0.65755 ( 4457) SS BOND : bond 0.00436 ( 5) SS BOND : angle 1.05613 ( 10) hydrogen bonds : bond 0.03587 ( 72) hydrogen bonds : angle 7.42926 ( 198) link_NAG-ASN : bond 0.00042 ( 1) link_NAG-ASN : angle 2.11932 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.121 Fit side-chains REVERT: A 465 GLU cc_start: 0.7008 (tp30) cc_final: 0.6758 (tp30) REVERT: A 466 ARG cc_start: 0.7874 (mtm-85) cc_final: 0.7430 (mtm-85) REVERT: A 486 PHE cc_start: 0.6608 (t80) cc_final: 0.6343 (t80) REVERT: H 1 GLN cc_start: 0.6809 (pp30) cc_final: 0.6529 (pp30) REVERT: H 103 ASP cc_start: 0.7661 (t0) cc_final: 0.7331 (m-30) outliers start: 7 outliers final: 5 residues processed: 48 average time/residue: 0.0755 time to fit residues: 4.4267 Evaluate side-chains 46 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.191964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.170838 restraints weight = 5176.267| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 2.77 r_work: 0.4253 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3282 Z= 0.159 Angle : 0.700 8.146 4470 Z= 0.374 Chirality : 0.045 0.179 480 Planarity : 0.005 0.050 572 Dihedral : 6.165 25.762 471 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.01 % Allowed : 15.23 % Favored : 82.76 % 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 are not related in a simple way. whole: -2.00 (0.40), residues: 400 helix: -1.90 (1.05), residues: 27 sheet: 0.08 (0.52), residues: 100 loop : -1.95 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 97 TYR 0.019 0.002 TYR L 35 PHE 0.012 0.002 PHE A 497 TRP 0.024 0.002 TRP H 36 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3276) covalent geometry : angle 0.69642 ( 4457) SS BOND : bond 0.00483 ( 5) SS BOND : angle 1.08101 ( 10) hydrogen bonds : bond 0.04368 ( 72) hydrogen bonds : angle 7.55612 ( 198) link_NAG-ASN : bond 0.00141 ( 1) link_NAG-ASN : angle 2.51364 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.148 Fit side-chains REVERT: A 466 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7490 (mtm-85) REVERT: A 486 PHE cc_start: 0.6587 (t80) cc_final: 0.6317 (t80) REVERT: A 509 ARG cc_start: 0.7050 (mtt180) cc_final: 0.6091 (mtp180) REVERT: H 103 ASP cc_start: 0.7711 (t0) cc_final: 0.7371 (m-30) outliers start: 7 outliers final: 7 residues processed: 55 average time/residue: 0.0775 time to fit residues: 5.0681 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.189605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.168555 restraints weight = 5177.514| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 2.75 r_work: 0.4235 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3282 Z= 0.198 Angle : 0.757 7.916 4470 Z= 0.407 Chirality : 0.046 0.208 480 Planarity : 0.005 0.050 572 Dihedral : 6.515 24.754 471 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.30 % Allowed : 16.38 % Favored : 81.32 % 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 are not related in a simple way. whole: -2.22 (0.40), residues: 400 helix: -2.04 (1.02), residues: 27 sheet: -0.03 (0.53), residues: 99 loop : -2.12 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 44 TYR 0.019 0.002 TYR L 35 PHE 0.012 0.002 PHE A 497 TRP 0.017 0.003 TRP H 36 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 3276) covalent geometry : angle 0.75268 ( 4457) SS BOND : bond 0.00550 ( 5) SS BOND : angle 1.21799 ( 10) hydrogen bonds : bond 0.04988 ( 72) hydrogen bonds : angle 7.79721 ( 198) link_NAG-ASN : bond 0.00221 ( 1) link_NAG-ASN : angle 2.71187 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.117 Fit side-chains REVERT: A 466 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7688 (mtm-85) REVERT: A 486 PHE cc_start: 0.6587 (t80) cc_final: 0.6304 (t80) REVERT: A 509 ARG cc_start: 0.7114 (mtt180) cc_final: 0.6148 (mtp180) REVERT: H 103 ASP cc_start: 0.7753 (t0) cc_final: 0.7444 (m-30) outliers start: 8 outliers final: 7 residues processed: 55 average time/residue: 0.0760 time to fit residues: 4.8995 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.3980 chunk 34 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 5 optimal weight: 0.0970 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.192622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.171720 restraints weight = 5204.451| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 2.75 r_work: 0.4269 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3282 Z= 0.131 Angle : 0.686 8.335 4470 Z= 0.365 Chirality : 0.044 0.154 480 Planarity : 0.005 0.048 572 Dihedral : 6.088 25.516 471 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.01 % Allowed : 16.38 % Favored : 81.61 % 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 are not related in a simple way. whole: -2.13 (0.41), residues: 400 helix: -2.26 (0.88), residues: 33 sheet: -0.13 (0.53), residues: 102 loop : -1.94 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 44 TYR 0.015 0.002 TYR L 35 PHE 0.012 0.001 PHE A 400 TRP 0.019 0.002 TRP H 36 HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3276) covalent geometry : angle 0.68253 ( 4457) SS BOND : bond 0.00448 ( 5) SS BOND : angle 1.12304 ( 10) hydrogen bonds : bond 0.03844 ( 72) hydrogen bonds : angle 7.63496 ( 198) link_NAG-ASN : bond 0.00039 ( 1) link_NAG-ASN : angle 2.16039 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1019.42 seconds wall clock time: 18 minutes 4.43 seconds (1084.43 seconds total)