Starting phenix.real_space_refine on Tue Feb 3 13:44:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lp1_63266/02_2026/9lp1_63266.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lp1_63266/02_2026/9lp1_63266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lp1_63266/02_2026/9lp1_63266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lp1_63266/02_2026/9lp1_63266.map" model { file = "/net/cci-nas-00/data/ceres_data/9lp1_63266/02_2026/9lp1_63266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lp1_63266/02_2026/9lp1_63266.cif" } resolution = 3.47 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2078 2.51 5 N 548 2.21 5 O 613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3254 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "B" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 770 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "C" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1556 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 180} Chain: "C" 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: 1.00, per 1000 atoms: 0.31 Number of scatterers: 3254 At special positions: 0 Unit cell: (62.08, 73.72, 98.94, 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 15 16.00 O 613 8.00 N 548 7.00 C 2078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 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 C 601 " - " ASN C 354 " Time building additional restraints: 0.15 Conformation dependent library (CDL) restraints added in 74.7 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 10 sheets defined 14.6% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.509A pdb=" N ARG A 31 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.578A pdb=" N LYS A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.650A pdb=" N THR A 90 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.605A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.979A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.563A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.611A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.274A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.986A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 18 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.986A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 70 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.539A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N MET A 34 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA5, first strand: chain 'B' and resid 8 through 11 removed outlier: 5.757A pdb=" N LEU B 9 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 88 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP B 34 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 11 removed outlier: 5.757A pdb=" N LEU B 9 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 17 through 22 removed outlier: 3.971A pdb=" N ASP B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER B 66 " --> pdb=" O ASP B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 358 removed outlier: 4.105A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 99 hydrogen bonds defined for protein. 222 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: 0.28 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 545 1.32 - 1.45: 994 1.45 - 1.57: 1790 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3347 Sorted by residual: bond pdb=" C PRO B 79 " pdb=" O PRO B 79 " ideal model delta sigma weight residual 1.237 1.199 0.039 1.32e-02 5.74e+03 8.61e+00 bond pdb=" N LEU B 11 " pdb=" CA LEU B 11 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.25e-02 6.40e+03 7.68e+00 bond pdb=" N ARG C 355 " pdb=" CA ARG C 355 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.23e-02 6.61e+03 6.97e+00 bond pdb=" CA SER B 12 " pdb=" CB SER B 12 " ideal model delta sigma weight residual 1.534 1.492 0.041 1.57e-02 4.06e+03 6.95e+00 bond pdb=" N LEU B 9 " pdb=" CA LEU B 9 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.84e+00 ... (remaining 3342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 4441 2.71 - 5.41: 92 5.41 - 8.12: 11 8.12 - 10.82: 3 10.82 - 13.53: 1 Bond angle restraints: 4548 Sorted by residual: angle pdb=" N LYS C 481 " pdb=" CA LYS C 481 " pdb=" C LYS C 481 " ideal model delta sigma weight residual 114.56 101.03 13.53 1.27e+00 6.20e-01 1.13e+02 angle pdb=" N ARG A 71 " pdb=" CA ARG A 71 " pdb=" C ARG A 71 " ideal model delta sigma weight residual 109.95 101.69 8.26 1.44e+00 4.82e-01 3.29e+01 angle pdb=" N ASP B 81 " pdb=" CA ASP B 81 " pdb=" C ASP B 81 " ideal model delta sigma weight residual 113.16 106.89 6.27 1.24e+00 6.50e-01 2.56e+01 angle pdb=" N ASN A 76 " pdb=" CA ASN A 76 " pdb=" C ASN A 76 " ideal model delta sigma weight residual 111.24 104.36 6.88 1.38e+00 5.25e-01 2.48e+01 angle pdb=" C PRO C 479 " pdb=" CA PRO C 479 " pdb=" CB PRO C 479 " ideal model delta sigma weight residual 111.64 117.60 -5.96 1.26e+00 6.30e-01 2.24e+01 ... (remaining 4543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 1823 17.84 - 35.68: 133 35.68 - 53.52: 18 53.52 - 71.36: 5 71.36 - 89.19: 2 Dihedral angle restraints: 1981 sinusoidal: 793 harmonic: 1188 Sorted by residual: dihedral pdb=" CA TRP C 353 " pdb=" C TRP C 353 " pdb=" N ASN C 354 " pdb=" CA ASN C 354 " ideal model delta harmonic sigma weight residual -180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" C CYS C 480 " pdb=" N CYS C 480 " pdb=" CA CYS C 480 " pdb=" CB CYS C 480 " ideal model delta harmonic sigma weight residual -122.60 -110.62 -11.98 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" C LYS C 458 " pdb=" N LYS C 458 " pdb=" CA LYS C 458 " pdb=" CB LYS C 458 " ideal model delta harmonic sigma weight residual -122.60 -112.69 -9.91 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 1978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 449 0.112 - 0.224: 22 0.224 - 0.336: 5 0.336 - 0.448: 0 0.448 - 0.559: 1 Chirality restraints: 477 Sorted by residual: chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 354 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" CA ASP A 72 " pdb=" N ASP A 72 " pdb=" C ASP A 72 " pdb=" CB ASP A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA LYS C 481 " pdb=" N LYS C 481 " pdb=" C LYS C 481 " pdb=" CB LYS C 481 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 474 not shown) Planarity restraints: 590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 601 " 0.272 2.00e-02 2.50e+03 2.35e-01 6.88e+02 pdb=" C7 NAG C 601 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG C 601 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG C 601 " -0.412 2.00e-02 2.50e+03 pdb=" O7 NAG C 601 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 477 " -0.009 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C ASN C 477 " 0.033 2.00e-02 2.50e+03 pdb=" O ASN C 477 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS C 478 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 75 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C LYS A 75 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS A 75 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN A 76 " 0.011 2.00e-02 2.50e+03 ... (remaining 587 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 67 2.67 - 3.23: 2960 3.23 - 3.78: 4636 3.78 - 4.34: 6591 4.34 - 4.90: 11228 Nonbonded interactions: 25482 Sorted by model distance: nonbonded pdb=" OH TYR A 99 " pdb=" OE2 GLU C 493 " model vdw 2.109 3.040 nonbonded pdb=" O ARG A 31 " pdb=" OH TYR C 473 " model vdw 2.163 3.040 nonbonded pdb=" OE1 GLU A 23 " pdb=" OG1 THR A 77 " model vdw 2.253 3.040 nonbonded pdb=" NH1 ARG A 97 " pdb=" OD2 ASP A 105 " model vdw 2.310 3.120 nonbonded pdb=" NH1 ARG A 66 " pdb=" O SER A 84 " model vdw 2.320 3.120 ... (remaining 25477 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: 6.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.210 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3354 Z= 0.314 Angle : 0.922 13.530 4563 Z= 0.584 Chirality : 0.066 0.559 477 Planarity : 0.011 0.235 589 Dihedral : 12.740 89.194 1213 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 4.17 % 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: -0.89 (0.40), residues: 406 helix: -3.88 (0.62), residues: 26 sheet: -0.44 (0.42), residues: 147 loop : -0.16 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 457 TYR 0.018 0.002 TYR B 35 PHE 0.015 0.002 PHE C 342 TRP 0.015 0.001 TRP A 107 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 3347) covalent geometry : angle 0.91911 ( 4548) SS BOND : bond 0.00525 ( 6) SS BOND : angle 1.19551 ( 12) hydrogen bonds : bond 0.22459 ( 90) hydrogen bonds : angle 10.68389 ( 222) link_NAG-ASN : bond 0.00941 ( 1) link_NAG-ASN : angle 2.66915 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.119 Fit side-chains REVERT: B 76 ARG cc_start: 0.7574 (tpp-160) cc_final: 0.7291 (ptp-170) REVERT: B 106 LYS cc_start: 0.5881 (mttt) cc_final: 0.4659 (mmmt) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0586 time to fit residues: 5.0537 Evaluate side-chains 61 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130682 restraints weight = 4241.374| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.35 r_work: 0.3373 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3354 Z= 0.204 Angle : 0.630 5.150 4563 Z= 0.325 Chirality : 0.050 0.225 477 Planarity : 0.005 0.033 589 Dihedral : 5.315 28.390 481 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.29 % Allowed : 6.02 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.82 (0.38), residues: 406 helix: -4.31 (0.49), residues: 20 sheet: -0.44 (0.43), residues: 129 loop : -0.19 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 457 TYR 0.018 0.002 TYR B 35 PHE 0.012 0.002 PHE B 70 TRP 0.014 0.002 TRP C 353 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 3347) covalent geometry : angle 0.62492 ( 4548) SS BOND : bond 0.00260 ( 6) SS BOND : angle 1.18421 ( 12) hydrogen bonds : bond 0.04241 ( 90) hydrogen bonds : angle 7.44246 ( 222) link_NAG-ASN : bond 0.00110 ( 1) link_NAG-ASN : angle 2.30965 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.127 Fit side-chains REVERT: B 76 ARG cc_start: 0.7927 (tpp-160) cc_final: 0.7124 (ptp-170) REVERT: B 106 LYS cc_start: 0.6267 (mttt) cc_final: 0.4847 (mmmt) outliers start: 8 outliers final: 4 residues processed: 66 average time/residue: 0.0589 time to fit residues: 4.8762 Evaluate side-chains 63 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.154895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128818 restraints weight = 4273.007| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.39 r_work: 0.3368 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3354 Z= 0.157 Angle : 0.557 6.125 4563 Z= 0.288 Chirality : 0.048 0.215 477 Planarity : 0.004 0.033 589 Dihedral : 5.739 52.080 481 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.01 % Allowed : 9.74 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.78 (0.39), residues: 406 helix: -4.28 (0.49), residues: 20 sheet: -0.52 (0.43), residues: 129 loop : -0.09 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 66 TYR 0.012 0.002 TYR B 48 PHE 0.010 0.001 PHE C 377 TRP 0.012 0.002 TRP C 353 HIS 0.002 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 3347) covalent geometry : angle 0.55433 ( 4548) SS BOND : bond 0.00160 ( 6) SS BOND : angle 1.09357 ( 12) hydrogen bonds : bond 0.03490 ( 90) hydrogen bonds : angle 6.75782 ( 222) link_NAG-ASN : bond 0.00272 ( 1) link_NAG-ASN : angle 1.35855 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.140 Fit side-chains REVERT: B 106 LYS cc_start: 0.6373 (mttt) cc_final: 0.4992 (mmmt) outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 0.0522 time to fit residues: 4.2801 Evaluate side-chains 62 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 16 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.156805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130645 restraints weight = 4310.655| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.43 r_work: 0.3366 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3354 Z= 0.164 Angle : 0.558 5.314 4563 Z= 0.288 Chirality : 0.048 0.196 477 Planarity : 0.004 0.032 589 Dihedral : 5.781 53.487 481 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.44 % Allowed : 12.32 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.85 (0.39), residues: 406 helix: -4.29 (0.49), residues: 20 sheet: -0.69 (0.43), residues: 126 loop : -0.07 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 466 TYR 0.012 0.001 TYR B 48 PHE 0.010 0.001 PHE C 377 TRP 0.011 0.002 TRP C 353 HIS 0.002 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 3347) covalent geometry : angle 0.55587 ( 4548) SS BOND : bond 0.00217 ( 6) SS BOND : angle 1.04104 ( 12) hydrogen bonds : bond 0.03233 ( 90) hydrogen bonds : angle 6.56999 ( 222) link_NAG-ASN : bond 0.00375 ( 1) link_NAG-ASN : angle 1.13196 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.142 Fit side-chains REVERT: B 106 LYS cc_start: 0.6460 (mttt) cc_final: 0.5165 (mmmt) outliers start: 12 outliers final: 10 residues processed: 62 average time/residue: 0.0400 time to fit residues: 3.3800 Evaluate side-chains 68 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.0370 chunk 3 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.157118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.131613 restraints weight = 4274.387| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.36 r_work: 0.3356 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3354 Z= 0.146 Angle : 0.541 5.342 4563 Z= 0.278 Chirality : 0.047 0.181 477 Planarity : 0.005 0.059 589 Dihedral : 5.625 53.157 481 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.15 % Allowed : 14.33 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.72 (0.39), residues: 406 helix: -4.19 (0.54), residues: 20 sheet: -0.61 (0.43), residues: 130 loop : 0.03 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 466 TYR 0.011 0.001 TYR B 48 PHE 0.009 0.001 PHE C 377 TRP 0.011 0.002 TRP C 353 HIS 0.002 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 3347) covalent geometry : angle 0.53886 ( 4548) SS BOND : bond 0.00212 ( 6) SS BOND : angle 1.00116 ( 12) hydrogen bonds : bond 0.03009 ( 90) hydrogen bonds : angle 6.25387 ( 222) link_NAG-ASN : bond 0.00266 ( 1) link_NAG-ASN : angle 0.82242 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: B 106 LYS cc_start: 0.6485 (mttt) cc_final: 0.5121 (mmmt) outliers start: 11 outliers final: 11 residues processed: 62 average time/residue: 0.0478 time to fit residues: 4.0049 Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.158708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132823 restraints weight = 4278.489| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.44 r_work: 0.3365 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3354 Z= 0.115 Angle : 0.507 5.274 4563 Z= 0.261 Chirality : 0.046 0.164 477 Planarity : 0.004 0.055 589 Dihedral : 5.388 52.782 481 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.72 % Allowed : 13.75 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.53 (0.40), residues: 406 helix: -4.15 (0.54), residues: 20 sheet: -0.51 (0.44), residues: 133 loop : 0.21 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 466 TYR 0.013 0.001 TYR A 103 PHE 0.008 0.001 PHE C 377 TRP 0.010 0.001 TRP C 353 HIS 0.001 0.000 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3347) covalent geometry : angle 0.50545 ( 4548) SS BOND : bond 0.00185 ( 6) SS BOND : angle 0.94640 ( 12) hydrogen bonds : bond 0.02770 ( 90) hydrogen bonds : angle 5.94158 ( 222) link_NAG-ASN : bond 0.00205 ( 1) link_NAG-ASN : angle 0.43335 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: B 106 LYS cc_start: 0.6598 (mttt) cc_final: 0.5219 (mmmt) outliers start: 13 outliers final: 12 residues processed: 64 average time/residue: 0.0514 time to fit residues: 4.2938 Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.157589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131986 restraints weight = 4383.325| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.41 r_work: 0.3360 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3354 Z= 0.154 Angle : 0.541 5.503 4563 Z= 0.280 Chirality : 0.047 0.180 477 Planarity : 0.005 0.059 589 Dihedral : 5.594 53.811 481 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.30 % Allowed : 14.33 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.62 (0.40), residues: 406 helix: -4.14 (0.55), residues: 20 sheet: -0.56 (0.44), residues: 133 loop : 0.14 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 466 TYR 0.018 0.001 TYR A 103 PHE 0.010 0.001 PHE B 70 TRP 0.011 0.002 TRP C 353 HIS 0.002 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3347) covalent geometry : angle 0.53877 ( 4548) SS BOND : bond 0.00183 ( 6) SS BOND : angle 1.02558 ( 12) hydrogen bonds : bond 0.02915 ( 90) hydrogen bonds : angle 6.06892 ( 222) link_NAG-ASN : bond 0.00322 ( 1) link_NAG-ASN : angle 0.83859 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: B 106 LYS cc_start: 0.6687 (mttt) cc_final: 0.5518 (mmmt) outliers start: 15 outliers final: 14 residues processed: 62 average time/residue: 0.0418 time to fit residues: 3.4721 Evaluate side-chains 72 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 31 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.0270 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.159624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133897 restraints weight = 4309.809| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.45 r_work: 0.3399 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3354 Z= 0.100 Angle : 0.496 5.462 4563 Z= 0.255 Chirality : 0.045 0.153 477 Planarity : 0.005 0.059 589 Dihedral : 5.213 52.471 481 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.87 % Allowed : 15.19 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.37 (0.41), residues: 406 helix: -4.12 (0.54), residues: 20 sheet: -0.44 (0.44), residues: 133 loop : 0.35 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 44 TYR 0.017 0.001 TYR A 103 PHE 0.008 0.001 PHE C 377 TRP 0.009 0.001 TRP C 353 HIS 0.001 0.000 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 3347) covalent geometry : angle 0.49406 ( 4548) SS BOND : bond 0.00178 ( 6) SS BOND : angle 0.91382 ( 12) hydrogen bonds : bond 0.02578 ( 90) hydrogen bonds : angle 5.70857 ( 222) link_NAG-ASN : bond 0.00111 ( 1) link_NAG-ASN : angle 0.36776 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7389 (mp0) REVERT: B 106 LYS cc_start: 0.6662 (mttt) cc_final: 0.5468 (mmmt) REVERT: C 337 PRO cc_start: 0.7428 (Cg_exo) cc_final: 0.7174 (Cg_endo) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.0561 time to fit residues: 4.5118 Evaluate side-chains 69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.0170 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.0770 chunk 35 optimal weight: 0.8980 overall best weight: 0.2776 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.160755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.134954 restraints weight = 4275.274| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.44 r_work: 0.3414 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3354 Z= 0.094 Angle : 0.490 5.201 4563 Z= 0.250 Chirality : 0.045 0.155 477 Planarity : 0.004 0.055 589 Dihedral : 5.090 52.356 481 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.58 % Allowed : 15.47 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.05 (0.41), residues: 406 helix: -4.06 (0.55), residues: 20 sheet: -0.12 (0.46), residues: 123 loop : 0.50 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 53 TYR 0.017 0.001 TYR A 103 PHE 0.007 0.001 PHE C 377 TRP 0.009 0.001 TRP C 436 HIS 0.001 0.000 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 3347) covalent geometry : angle 0.48866 ( 4548) SS BOND : bond 0.00189 ( 6) SS BOND : angle 0.92780 ( 12) hydrogen bonds : bond 0.02461 ( 90) hydrogen bonds : angle 5.50830 ( 222) link_NAG-ASN : bond 0.00050 ( 1) link_NAG-ASN : angle 0.52675 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7388 (mp0) REVERT: B 53 ARG cc_start: 0.7574 (mtm-85) cc_final: 0.7330 (mtm-85) REVERT: B 106 LYS cc_start: 0.6598 (mttt) cc_final: 0.5413 (mmmt) REVERT: C 337 PRO cc_start: 0.7343 (Cg_exo) cc_final: 0.7095 (Cg_endo) outliers start: 9 outliers final: 8 residues processed: 64 average time/residue: 0.0374 time to fit residues: 3.0741 Evaluate side-chains 69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.157286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131282 restraints weight = 4320.261| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.46 r_work: 0.3340 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3354 Z= 0.160 Angle : 0.547 5.414 4563 Z= 0.283 Chirality : 0.047 0.184 477 Planarity : 0.005 0.057 589 Dihedral : 5.513 53.421 481 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.44 % Allowed : 14.90 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.32 (0.41), residues: 406 helix: -4.11 (0.55), residues: 20 sheet: -0.41 (0.44), residues: 133 loop : 0.39 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 53 TYR 0.024 0.002 TYR A 103 PHE 0.012 0.002 PHE A 67 TRP 0.011 0.002 TRP C 353 HIS 0.002 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3347) covalent geometry : angle 0.54503 ( 4548) SS BOND : bond 0.00164 ( 6) SS BOND : angle 1.08158 ( 12) hydrogen bonds : bond 0.02893 ( 90) hydrogen bonds : angle 5.92012 ( 222) link_NAG-ASN : bond 0.00327 ( 1) link_NAG-ASN : angle 0.79516 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7383 (mtm-85) REVERT: B 106 LYS cc_start: 0.6678 (mttt) cc_final: 0.5489 (mmmt) outliers start: 12 outliers final: 12 residues processed: 62 average time/residue: 0.0324 time to fit residues: 2.6653 Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 26 optimal weight: 0.0000 chunk 5 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 overall best weight: 0.3584 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.159314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134006 restraints weight = 4390.497| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.38 r_work: 0.3412 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3354 Z= 0.108 Angle : 0.504 5.395 4563 Z= 0.259 Chirality : 0.045 0.160 477 Planarity : 0.005 0.063 589 Dihedral : 5.218 52.592 481 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.44 % Allowed : 15.19 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.18 (0.42), residues: 406 helix: -4.05 (0.56), residues: 20 sheet: -0.33 (0.45), residues: 133 loop : 0.51 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 53 TYR 0.020 0.001 TYR A 103 PHE 0.011 0.001 PHE A 67 TRP 0.009 0.001 TRP C 353 HIS 0.001 0.000 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3347) covalent geometry : angle 0.50244 ( 4548) SS BOND : bond 0.00177 ( 6) SS BOND : angle 0.96867 ( 12) hydrogen bonds : bond 0.02568 ( 90) hydrogen bonds : angle 5.65126 ( 222) link_NAG-ASN : bond 0.00136 ( 1) link_NAG-ASN : angle 0.37464 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 994.17 seconds wall clock time: 17 minutes 47.11 seconds (1067.11 seconds total)