Starting phenix.real_space_refine on Tue Aug 4 23:47:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k66_36918/08_2026/8k66_36918.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k66_36918/08_2026/8k66_36918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k66_36918/08_2026/8k66_36918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k66_36918/08_2026/8k66_36918.map" model { file = "/net/cci-nas-00/data/ceres_data/8k66_36918/08_2026/8k66_36918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k66_36918/08_2026/8k66_36918.cif" } resolution = 2.53 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= 0.001 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 34 5.16 5 Na 4 4.78 5 C 5070 2.51 5 N 1120 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7620 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3514 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 443, 3511 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 443, 3511 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424} Chain breaks: 2 bond proxies already assigned to first conformer: 3595 Chain: "B" Number of atoms: 3514 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 443, 3511 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 443, 3511 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424} Chain breaks: 2 bond proxies already assigned to first conformer: 3595 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 231 Unusual residues: {' NA': 2, 'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'T7X:plan-5': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 231 Unusual residues: {' NA': 2, 'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'T7X:plan-5': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Time building chain proxies: 2.46, per 1000 atoms: 0.32 Number of scatterers: 7620 At special positions: 0 Unit cell: (104.498, 110.423, 82.4135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 6 15.00 Na 4 11.00 O 1386 8.00 N 1120 7.00 C 5070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG ACYS A 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG ACYS B 488 " distance=2.05 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 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 594.0 milliseconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1668 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 77.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 22 through 38 removed outlier: 3.803A pdb=" N PHE A 26 " --> pdb=" O TYR A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 62 Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 181 through 214 Processing helix chain 'A' and resid 214 through 225 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 227 through 241 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 258 through 273 Processing helix chain 'A' and resid 275 through 292 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.684A pdb=" N LYS A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.608A pdb=" N GLU A 305 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 340 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 349 through 364 Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 378 through 391 removed outlier: 3.564A pdb=" N LEU A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 423 Processing helix chain 'A' and resid 425 through 441 Processing helix chain 'A' and resid 441 through 448 Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.535A pdb=" N LEU A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 516 removed outlier: 3.552A pdb=" N LEU A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 39 through 62 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 181 through 214 Processing helix chain 'B' and resid 214 through 225 Proline residue: B 220 - end of helix Processing helix chain 'B' and resid 227 through 241 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 258 through 273 Processing helix chain 'B' and resid 275 through 292 Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.599A pdb=" N LYS B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 340 Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 349 through 364 Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 378 through 391 removed outlier: 3.535A pdb=" N LEU B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 423 Processing helix chain 'B' and resid 425 through 441 Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.533A pdb=" N LEU B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 500 through 516 removed outlier: 3.550A pdb=" N LEU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528 486 hydrogen bonds defined for protein. 1389 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: 0.97 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1052 1.31 - 1.44: 2090 1.44 - 1.57: 4466 1.57 - 1.71: 12 1.71 - 1.84: 58 Bond restraints: 7678 Sorted by residual: bond pdb=" CA SER A 87 " pdb=" CB SER A 87 " ideal model delta sigma weight residual 1.531 1.461 0.070 1.56e-02 4.11e+03 2.04e+01 bond pdb=" CA SER B 87 " pdb=" CB SER B 87 " ideal model delta sigma weight residual 1.531 1.462 0.070 1.56e-02 4.11e+03 1.99e+01 bond pdb=" C11 T7X B 704 " pdb=" O18 T7X B 704 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C11 T7X A 603 " pdb=" O18 T7X A 603 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" N ILE A 90 " pdb=" CA ILE A 90 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.14e-02 7.69e+03 1.16e+01 ... (remaining 7673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 10176 3.20 - 6.40: 208 6.40 - 9.60: 28 9.60 - 12.80: 2 12.80 - 15.99: 6 Bond angle restraints: 10420 Sorted by residual: angle pdb=" O1 T7X B 704 " pdb=" P1 T7X B 704 " pdb=" O13 T7X B 704 " ideal model delta sigma weight residual 94.60 110.59 -15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" O1 T7X A 603 " pdb=" P1 T7X A 603 " pdb=" O13 T7X A 603 " ideal model delta sigma weight residual 94.60 110.57 -15.97 3.00e+00 1.11e-01 2.83e+01 angle pdb=" O11 PTY B 705 " pdb=" P1 PTY B 705 " pdb=" O14 PTY B 705 " ideal model delta sigma weight residual 92.90 108.67 -15.77 3.00e+00 1.11e-01 2.76e+01 angle pdb=" O11 PTY A 604 " pdb=" P1 PTY A 604 " pdb=" O14 PTY A 604 " ideal model delta sigma weight residual 92.90 108.64 -15.74 3.00e+00 1.11e-01 2.75e+01 angle pdb=" O12 PC1 B 701 " pdb=" P PC1 B 701 " pdb=" O14 PC1 B 701 " ideal model delta sigma weight residual 123.67 110.29 13.38 3.00e+00 1.11e-01 1.99e+01 ... (remaining 10415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.86: 4421 24.86 - 49.71: 319 49.71 - 74.57: 62 74.57 - 99.43: 7 99.43 - 124.29: 7 Dihedral angle restraints: 4816 sinusoidal: 2234 harmonic: 2582 Sorted by residual: dihedral pdb=" CA ILE A 300 " pdb=" C ILE A 300 " pdb=" N LYS A 301 " pdb=" CA LYS A 301 " ideal model delta harmonic sigma weight residual 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" C15 T7X B 704 " pdb=" C16 T7X B 704 " pdb=" C17 T7X B 704 " pdb=" C18 T7X B 704 " ideal model delta sinusoidal sigma weight residual 111.73 -123.98 -124.29 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" C15 T7X A 603 " pdb=" C16 T7X A 603 " pdb=" C17 T7X A 603 " pdb=" C18 T7X A 603 " ideal model delta sinusoidal sigma weight residual 111.73 -124.04 -124.23 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 4813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.957: 1226 0.957 - 1.914: 0 1.914 - 2.871: 0 2.871 - 3.827: 0 3.827 - 4.784: 2 Chirality restraints: 1228 Sorted by residual: chirality pdb=" C1 T7X B 704 " pdb=" C2 T7X B 704 " pdb=" C6 T7X B 704 " pdb=" O1 T7X B 704 " both_signs ideal model delta sigma weight residual False -2.42 2.37 -4.78 2.00e-01 2.50e+01 5.72e+02 chirality pdb=" C1 T7X A 603 " pdb=" C2 T7X A 603 " pdb=" C6 T7X A 603 " pdb=" O1 T7X A 603 " both_signs ideal model delta sigma weight residual False -2.42 2.36 -4.78 2.00e-01 2.50e+01 5.72e+02 chirality pdb=" CBG Y01 B 702 " pdb=" CAQ Y01 B 702 " pdb=" CBD Y01 B 702 " pdb=" CBI Y01 B 702 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1225 not shown) Planarity restraints: 1202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 249 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C ASN B 249 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN B 249 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU B 250 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 246 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO B 247 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 246 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 247 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " 0.021 5.00e-02 4.00e+02 ... (remaining 1199 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 85 2.58 - 3.16: 6031 3.16 - 3.74: 12201 3.74 - 4.32: 18197 4.32 - 4.90: 29062 Nonbonded interactions: 65576 Sorted by model distance: nonbonded pdb=" NH2 ARG A 478 " pdb=" O HOH A 701 " model vdw 1.997 3.120 nonbonded pdb=" O LEU A 245 " pdb=" O HOH A 702 " model vdw 2.011 3.040 nonbonded pdb=" O LEU B 86 " pdb="NA NA B 707 " model vdw 2.027 2.470 nonbonded pdb=" O HOH A 750 " pdb=" O HOH A 762 " model vdw 2.039 3.040 nonbonded pdb=" O HOH B 819 " pdb=" O HOH B 860 " model vdw 2.042 3.040 ... (remaining 65571 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 487 or resid 489 through 530 or resid 602 or re \ sid 607 through 608)) selection = (chain 'B' and (resid 22 through 487 or resid 489 through 530 or resid 702 or re \ sid 707 through 708)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.280 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 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:9.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 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 : 0.006 0.073 7680 Z= 0.305 Angle : 1.051 15.995 10424 Z= 0.469 Chirality : 0.199 4.784 1228 Planarity : 0.004 0.045 1202 Dihedral : 17.656 124.285 3142 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.20 % Allowed : 13.68 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: -0.42 (0.26), residues: 876 helix: 0.39 (0.19), residues: 626 sheet: None (None), residues: 0 loop : -1.86 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 294 TYR 0.015 0.002 TYR B 195 PHE 0.013 0.001 PHE B 196 TRP 0.006 0.001 TRP A 285 HIS 0.002 0.001 HIS B 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.30 ( 7678) covalent geometry : angle 1.04939 / 0.47 (10420) SS BOND : bond 0.01487 / 0.75 ( 2) SS BOND : angle 2.95067 / 1.81 ( 4) hydrogen bonds : bond 0.13957 / 9.19 ( 486) hydrogen bonds : angle 4.67253 / 3.29 ( 1389) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.317 Fit side-chains REVERT: A 61 PHE cc_start: 0.7266 (m-10) cc_final: 0.6881 (m-80) REVERT: A 63 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7481 (mmpt) REVERT: A 185 ARG cc_start: 0.7666 (ttp-170) cc_final: 0.7233 (ttm-80) REVERT: A 304 GLU cc_start: 0.7311 (pm20) cc_final: 0.6993 (mp0) REVERT: A 414 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.6036 (tptp) REVERT: A 422 LEU cc_start: 0.8354 (tp) cc_final: 0.8146 (tp) REVERT: B 70 ARG cc_start: 0.6812 (mtm-85) cc_final: 0.6486 (mpp-170) REVERT: B 185 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7343 (ttm-80) REVERT: B 422 LEU cc_start: 0.8354 (tp) cc_final: 0.8137 (tp) outliers start: 25 outliers final: 9 residues processed: 141 average time/residue: 0.6232 time to fit residues: 92.0256 Evaluate side-chains 114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 415 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 ASN A 39 HIS A 200 HIS A 273 ASN A 421 ASN A 483 HIS B 25 ASN B 31 HIS B 39 HIS B 200 HIS B 273 ASN B 421 ASN B 483 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.123404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.095115 restraints weight = 10159.576| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.38 r_work: 0.2817 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7680 Z= 0.131 Angle : 0.552 6.384 10424 Z= 0.284 Chirality : 0.039 0.126 1228 Planarity : 0.004 0.041 1202 Dihedral : 13.666 116.904 1567 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.94 % Allowed : 14.58 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 1.42 (0.28), residues: 876 helix: 1.70 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -1.07 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 528 TYR 0.015 0.002 TYR A 195 PHE 0.012 0.001 PHE B 196 TRP 0.006 0.001 TRP A 285 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7678) covalent geometry : angle 0.54925 / 0.28 (10420) SS BOND : bond 0.01401 / 0.70 ( 2) SS BOND : angle 2.86207 / 1.72 ( 4) hydrogen bonds : bond 0.04419 / 2.88 ( 486) hydrogen bonds : angle 3.80072 / 2.69 ( 1389) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.286 Fit side-chains REVERT: A 61 PHE cc_start: 0.7729 (m-10) cc_final: 0.7294 (m-80) REVERT: A 68 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6988 (mm-30) REVERT: A 185 ARG cc_start: 0.7815 (ttp-170) cc_final: 0.6986 (ttm-80) REVERT: A 213 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7258 (mmt180) REVERT: A 304 GLU cc_start: 0.7143 (pm20) cc_final: 0.6792 (mp0) REVERT: A 422 LEU cc_start: 0.8297 (tp) cc_final: 0.8085 (tp) REVERT: A 529 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9035 (mp) REVERT: B 70 ARG cc_start: 0.7153 (mtm-85) cc_final: 0.6946 (mpp80) REVERT: B 185 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7056 (ttm-80) REVERT: B 422 LEU cc_start: 0.8308 (tp) cc_final: 0.8087 (tp) REVERT: B 529 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9041 (mp) outliers start: 21 outliers final: 13 residues processed: 121 average time/residue: 0.6118 time to fit residues: 78.1504 Evaluate side-chains 114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN B 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.094747 restraints weight = 11629.598| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.47 r_work: 0.2776 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7680 Z= 0.127 Angle : 0.533 6.032 10424 Z= 0.276 Chirality : 0.039 0.128 1228 Planarity : 0.004 0.041 1202 Dihedral : 12.787 106.273 1552 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.81 % Allowed : 15.09 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 1.94 (0.29), residues: 876 helix: 2.05 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.83 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 528 TYR 0.015 0.002 TYR A 195 PHE 0.013 0.001 PHE B 196 TRP 0.005 0.001 TRP A 42 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 7678) covalent geometry : angle 0.52981 / 0.28 (10420) SS BOND : bond 0.01307 / 0.65 ( 2) SS BOND : angle 2.87362 / 1.73 ( 4) hydrogen bonds : bond 0.04311 / 2.80 ( 486) hydrogen bonds : angle 3.66182 / 2.58 ( 1389) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.297 Fit side-chains REVERT: A 61 PHE cc_start: 0.7669 (m-10) cc_final: 0.7205 (m-80) REVERT: A 68 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6946 (mm-30) REVERT: A 70 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7113 (ptp90) REVERT: A 185 ARG cc_start: 0.7821 (ttp-170) cc_final: 0.6941 (ttm-80) REVERT: A 304 GLU cc_start: 0.7098 (pm20) cc_final: 0.6707 (mp0) REVERT: A 422 LEU cc_start: 0.8275 (tp) cc_final: 0.8064 (tp) REVERT: A 478 ARG cc_start: 0.8126 (mtp180) cc_final: 0.7693 (mtm180) REVERT: A 529 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9025 (mp) REVERT: B 185 ARG cc_start: 0.7775 (ttp-170) cc_final: 0.7029 (ttm-80) REVERT: B 422 LEU cc_start: 0.8295 (tp) cc_final: 0.8075 (tp) REVERT: B 529 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9034 (mp) outliers start: 20 outliers final: 8 residues processed: 119 average time/residue: 0.5733 time to fit residues: 71.8974 Evaluate side-chains 114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN B 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.123714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.096415 restraints weight = 8673.050| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.27 r_work: 0.2875 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 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 : 0.003 0.025 7680 Z= 0.118 Angle : 0.514 5.303 10424 Z= 0.268 Chirality : 0.038 0.125 1228 Planarity : 0.004 0.040 1202 Dihedral : 12.176 104.228 1546 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.81 % Allowed : 15.22 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 2.17 (0.29), residues: 876 helix: 2.21 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.75 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 528 TYR 0.015 0.002 TYR A 195 PHE 0.013 0.001 PHE B 196 TRP 0.005 0.001 TRP A 285 HIS 0.002 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7678) covalent geometry : angle 0.51065 / 0.27 (10420) SS BOND : bond 0.01273 / 0.64 ( 2) SS BOND : angle 2.84413 / 1.71 ( 4) hydrogen bonds : bond 0.04027 / 2.62 ( 486) hydrogen bonds : angle 3.58261 / 2.53 ( 1389) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.215 Fit side-chains REVERT: A 61 PHE cc_start: 0.7663 (m-10) cc_final: 0.7151 (m-80) REVERT: A 68 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6964 (mm-30) REVERT: A 70 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7120 (ptp90) REVERT: A 185 ARG cc_start: 0.7808 (ttp-170) cc_final: 0.6962 (ttm-80) REVERT: A 304 GLU cc_start: 0.7130 (pm20) cc_final: 0.6747 (mp0) REVERT: A 422 LEU cc_start: 0.8303 (tp) cc_final: 0.8087 (tp) REVERT: A 478 ARG cc_start: 0.8156 (mtp180) cc_final: 0.7731 (mtm180) REVERT: A 486 SER cc_start: 0.7504 (OUTLIER) cc_final: 0.7161 (p) REVERT: A 529 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9074 (mp) REVERT: B 65 SER cc_start: 0.7831 (m) cc_final: 0.7596 (p) REVERT: B 185 ARG cc_start: 0.7764 (ttp-170) cc_final: 0.7050 (ttm-80) REVERT: B 422 LEU cc_start: 0.8283 (tp) cc_final: 0.8060 (tp) REVERT: B 486 SER cc_start: 0.7532 (OUTLIER) cc_final: 0.7166 (p) REVERT: B 529 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9081 (mp) outliers start: 20 outliers final: 10 residues processed: 118 average time/residue: 0.6247 time to fit residues: 77.7148 Evaluate side-chains 116 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.0000 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN B 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.123055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.095871 restraints weight = 9213.422| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.31 r_work: 0.2806 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7680 Z= 0.121 Angle : 0.519 5.319 10424 Z= 0.271 Chirality : 0.038 0.126 1228 Planarity : 0.004 0.040 1202 Dihedral : 11.907 103.162 1546 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.43 % Allowed : 15.35 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 2.21 (0.29), residues: 876 helix: 2.24 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.70 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 528 TYR 0.015 0.002 TYR A 195 PHE 0.013 0.001 PHE B 196 TRP 0.005 0.001 TRP A 42 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 7678) covalent geometry : angle 0.51562 / 0.27 (10420) SS BOND : bond 0.01270 / 0.64 ( 2) SS BOND : angle 2.92032 / 1.75 ( 4) hydrogen bonds : bond 0.04125 / 2.69 ( 486) hydrogen bonds : angle 3.58606 / 2.53 ( 1389) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.292 Fit side-chains REVERT: A 61 PHE cc_start: 0.7608 (m-10) cc_final: 0.7076 (m-80) REVERT: A 68 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6965 (mm-30) REVERT: A 70 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7092 (ptp90) REVERT: A 185 ARG cc_start: 0.7812 (ttp-170) cc_final: 0.6958 (ttm-80) REVERT: A 304 GLU cc_start: 0.7142 (pm20) cc_final: 0.6803 (mp0) REVERT: A 422 LEU cc_start: 0.8314 (tp) cc_final: 0.8105 (tp) REVERT: A 478 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7687 (mtm180) REVERT: A 486 SER cc_start: 0.7488 (OUTLIER) cc_final: 0.7154 (p) REVERT: A 529 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9031 (mp) REVERT: B 65 SER cc_start: 0.7806 (m) cc_final: 0.7578 (p) REVERT: B 185 ARG cc_start: 0.7766 (ttp-170) cc_final: 0.7036 (ttm-80) REVERT: B 422 LEU cc_start: 0.8306 (tp) cc_final: 0.8105 (tp) REVERT: B 486 SER cc_start: 0.7404 (OUTLIER) cc_final: 0.7137 (p) REVERT: B 529 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9031 (mp) outliers start: 17 outliers final: 11 residues processed: 118 average time/residue: 0.5709 time to fit residues: 71.0504 Evaluate side-chains 116 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN B 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.118599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.089615 restraints weight = 10557.354| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.48 r_work: 0.2746 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7680 Z= 0.163 Angle : 0.583 5.421 10424 Z= 0.302 Chirality : 0.040 0.138 1228 Planarity : 0.005 0.042 1202 Dihedral : 12.024 104.170 1546 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.43 % Allowed : 15.60 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 1.97 (0.28), residues: 876 helix: 2.08 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -0.80 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 528 TYR 0.017 0.002 TYR A 195 PHE 0.014 0.002 PHE B 196 TRP 0.006 0.001 TRP A 42 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 7678) covalent geometry : angle 0.57948 / 0.30 (10420) SS BOND : bond 0.01378 / 0.69 ( 2) SS BOND : angle 3.30751 / 1.97 ( 4) hydrogen bonds : bond 0.04850 / 3.16 ( 486) hydrogen bonds : angle 3.69138 / 2.61 ( 1389) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.208 Fit side-chains REVERT: A 61 PHE cc_start: 0.7710 (m-10) cc_final: 0.7253 (m-80) REVERT: A 68 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6979 (mm-30) REVERT: A 70 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7136 (ptp90) REVERT: A 185 ARG cc_start: 0.7822 (ttp-170) cc_final: 0.6985 (ttm-80) REVERT: A 304 GLU cc_start: 0.7165 (pm20) cc_final: 0.6761 (mp0) REVERT: A 478 ARG cc_start: 0.8168 (mtp180) cc_final: 0.7690 (mtm180) REVERT: A 529 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9011 (mp) REVERT: B 65 SER cc_start: 0.7822 (m) cc_final: 0.7571 (p) REVERT: B 185 ARG cc_start: 0.7813 (ttp-170) cc_final: 0.7066 (ttm-80) REVERT: B 529 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9009 (mp) outliers start: 17 outliers final: 10 residues processed: 118 average time/residue: 0.5472 time to fit residues: 68.0083 Evaluate side-chains 116 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN A 421 ASN B 421 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.120931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.092714 restraints weight = 8594.491| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.36 r_work: 0.2803 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7680 Z= 0.117 Angle : 0.517 6.249 10424 Z= 0.270 Chirality : 0.038 0.127 1228 Planarity : 0.004 0.039 1202 Dihedral : 11.617 103.392 1546 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.81 % Allowed : 15.60 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 2.25 (0.29), residues: 876 helix: 2.26 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.66 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 528 TYR 0.015 0.002 TYR B 195 PHE 0.013 0.001 PHE B 196 TRP 0.005 0.001 TRP A 499 HIS 0.002 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 7678) covalent geometry : angle 0.51377 / 0.27 (10420) SS BOND : bond 0.01232 / 0.62 ( 2) SS BOND : angle 2.92423 / 1.75 ( 4) hydrogen bonds : bond 0.03949 / 2.57 ( 486) hydrogen bonds : angle 3.56850 / 2.51 ( 1389) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.179 Fit side-chains REVERT: A 61 PHE cc_start: 0.7599 (m-10) cc_final: 0.7080 (m-80) REVERT: A 68 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6945 (mm-30) REVERT: A 70 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7101 (ptp90) REVERT: A 185 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.6930 (ttm-80) REVERT: A 304 GLU cc_start: 0.7134 (pm20) cc_final: 0.6745 (mp0) REVERT: A 478 ARG cc_start: 0.8106 (mtp180) cc_final: 0.7626 (mtm180) REVERT: A 529 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8954 (mp) REVERT: B 65 SER cc_start: 0.7751 (m) cc_final: 0.7522 (p) REVERT: B 185 ARG cc_start: 0.7751 (ttp-170) cc_final: 0.7007 (ttm-80) REVERT: B 529 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9006 (mp) outliers start: 20 outliers final: 10 residues processed: 120 average time/residue: 0.5728 time to fit residues: 72.3722 Evaluate side-chains 115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 53 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN B 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.123213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.095724 restraints weight = 8077.377| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.30 r_work: 0.2865 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7680 Z= 0.099 Angle : 0.484 5.252 10424 Z= 0.253 Chirality : 0.037 0.121 1228 Planarity : 0.004 0.038 1202 Dihedral : 11.164 102.272 1546 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.92 % Allowed : 16.62 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 2.49 (0.29), residues: 876 helix: 2.45 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.62 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 528 TYR 0.014 0.002 TYR B 195 PHE 0.012 0.001 PHE B 196 TRP 0.006 0.001 TRP A 285 HIS 0.001 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 7678) covalent geometry : angle 0.48085 / 0.25 (10420) SS BOND : bond 0.01175 / 0.59 ( 2) SS BOND : angle 2.72303 / 1.62 ( 4) hydrogen bonds : bond 0.03509 / 2.28 ( 486) hydrogen bonds : angle 3.49678 / 2.45 ( 1389) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.225 Fit side-chains REVERT: A 32 ARG cc_start: 0.7332 (mpt-90) cc_final: 0.6486 (mtp85) REVERT: A 61 PHE cc_start: 0.7519 (m-10) cc_final: 0.6918 (m-80) REVERT: A 68 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6965 (mm-30) REVERT: A 70 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.7079 (ptp90) REVERT: A 185 ARG cc_start: 0.7756 (ttp-170) cc_final: 0.6943 (ttm-80) REVERT: A 304 GLU cc_start: 0.7156 (pm20) cc_final: 0.6710 (mp0) REVERT: A 478 ARG cc_start: 0.8073 (mtp180) cc_final: 0.7815 (mtm180) REVERT: B 65 SER cc_start: 0.7720 (m) cc_final: 0.7519 (p) REVERT: B 185 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7027 (ttm-80) REVERT: B 295 GLU cc_start: 0.8116 (mp0) cc_final: 0.7811 (mp0) REVERT: B 304 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6762 (pm20) outliers start: 13 outliers final: 6 residues processed: 109 average time/residue: 0.5770 time to fit residues: 66.1175 Evaluate side-chains 110 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.119383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.091956 restraints weight = 7878.495| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.28 r_work: 0.2819 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7680 Z= 0.153 Angle : 0.565 5.412 10424 Z= 0.292 Chirality : 0.040 0.134 1228 Planarity : 0.004 0.042 1202 Dihedral : 11.652 104.398 1546 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.05 % Allowed : 16.11 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 2.17 (0.28), residues: 876 helix: 2.22 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -0.73 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 528 TYR 0.016 0.002 TYR A 195 PHE 0.014 0.001 PHE B 196 TRP 0.007 0.001 TRP A 499 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 7678) covalent geometry : angle 0.56129 / 0.29 (10420) SS BOND : bond 0.01278 / 0.64 ( 2) SS BOND : angle 3.22764 / 1.91 ( 4) hydrogen bonds : bond 0.04633 / 3.02 ( 486) hydrogen bonds : angle 3.63051 / 2.56 ( 1389) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.297 Fit side-chains REVERT: A 61 PHE cc_start: 0.7659 (m-10) cc_final: 0.7151 (m-80) REVERT: A 68 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6965 (mm-30) REVERT: A 70 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7159 (ptp90) REVERT: A 185 ARG cc_start: 0.7781 (ttp-170) cc_final: 0.6969 (ttm-80) REVERT: A 295 GLU cc_start: 0.7994 (mp0) cc_final: 0.7732 (mp0) REVERT: A 304 GLU cc_start: 0.7231 (pm20) cc_final: 0.6831 (mp0) REVERT: A 478 ARG cc_start: 0.8136 (mtp180) cc_final: 0.7660 (mtm180) REVERT: B 65 SER cc_start: 0.7815 (m) cc_final: 0.7590 (p) REVERT: B 185 ARG cc_start: 0.7773 (ttp-170) cc_final: 0.7054 (ttm-80) REVERT: B 295 GLU cc_start: 0.8108 (mp0) cc_final: 0.7791 (mp0) outliers start: 14 outliers final: 10 residues processed: 115 average time/residue: 0.5439 time to fit residues: 66.0031 Evaluate side-chains 120 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 80 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.096046 restraints weight = 9132.499| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.35 r_work: 0.2838 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7680 Z= 0.097 Angle : 0.485 5.251 10424 Z= 0.253 Chirality : 0.037 0.125 1228 Planarity : 0.004 0.038 1202 Dihedral : 11.242 103.122 1546 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.53 % Allowed : 17.01 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 2.49 (0.29), residues: 876 helix: 2.46 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.67 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 528 TYR 0.013 0.002 TYR A 195 PHE 0.013 0.001 PHE B 196 TRP 0.007 0.001 TRP A 285 HIS 0.001 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 ( 7678) covalent geometry : angle 0.48217 / 0.25 (10420) SS BOND : bond 0.01140 / 0.57 ( 2) SS BOND : angle 2.82519 / 1.68 ( 4) hydrogen bonds : bond 0.03477 / 2.27 ( 486) hydrogen bonds : angle 3.51173 / 2.47 ( 1389) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.271 Fit side-chains REVERT: A 32 ARG cc_start: 0.7336 (mpt-90) cc_final: 0.6489 (mtp85) REVERT: A 61 PHE cc_start: 0.7562 (m-10) cc_final: 0.6990 (m-80) REVERT: A 68 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6969 (mm-30) REVERT: A 70 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7133 (ptp90) REVERT: A 185 ARG cc_start: 0.7763 (ttp-170) cc_final: 0.6937 (ttm-80) REVERT: A 304 GLU cc_start: 0.7182 (pm20) cc_final: 0.6787 (mp0) REVERT: A 478 ARG cc_start: 0.8091 (mtp180) cc_final: 0.7764 (mtm180) REVERT: B 65 SER cc_start: 0.7739 (m) cc_final: 0.7527 (p) REVERT: B 185 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7019 (ttm-80) REVERT: B 295 GLU cc_start: 0.8100 (mp0) cc_final: 0.7770 (mp0) REVERT: B 304 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6792 (pm20) outliers start: 10 outliers final: 7 residues processed: 110 average time/residue: 0.5783 time to fit residues: 66.9135 Evaluate side-chains 112 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 304 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 62 optimal weight: 0.0000 chunk 42 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.093660 restraints weight = 8370.980| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.30 r_work: 0.2807 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7680 Z= 0.124 Angle : 0.524 5.348 10424 Z= 0.272 Chirality : 0.038 0.133 1228 Planarity : 0.004 0.038 1202 Dihedral : 11.331 103.632 1546 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.79 % Allowed : 16.37 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.24 % 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: 2.39 (0.29), residues: 876 helix: 2.37 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.65 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 528 TYR 0.015 0.002 TYR A 195 PHE 0.013 0.001 PHE B 196 TRP 0.006 0.001 TRP B 499 HIS 0.002 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 7678) covalent geometry : angle 0.52081 / 0.27 (10420) SS BOND : bond 0.01198 / 0.60 ( 2) SS BOND : angle 2.94060 / 1.74 ( 4) hydrogen bonds : bond 0.04111 / 2.68 ( 486) hydrogen bonds : angle 3.54330 / 2.49 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3242.43 seconds wall clock time: 55 minutes 57.57 seconds (3357.57 seconds total)