Starting phenix.real_space_refine on Thu Jul 2 07:30:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k66_36918/07_2026/8k66_36918.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k66_36918/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8k66_36918/07_2026/8k66_36918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k66_36918/07_2026/8k66_36918.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k66_36918/07_2026/8k66_36918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k66_36918/07_2026/8k66_36918.map" } 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-dev-6108/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, 229 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 2 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, 229 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain breaks: 2 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: 2.13, per 1000 atoms: 0.28 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: 0.77 Conformation dependent library (CDL) restraints added in 323.0 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: 0.11 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: 0.83 Time building geometry restraints manager: 0.86 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 3.210 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: 9.210 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.550 Find NCS groups from input model: 0.150 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.080 ------------------------------------------------------------------------------- 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 : 0.278 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: 0.5631 time to fit residues: 83.3787 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 : 0.219 ------------------------------------------------------------------------------- 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: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.122980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.094899 restraints weight = 9899.074| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.36 r_work: 0.2808 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7680 Z= 0.132 Angle : 0.551 6.387 10424 Z= 0.284 Chirality : 0.039 0.128 1228 Planarity : 0.004 0.040 1202 Dihedral : 13.749 117.536 1567 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.94 % Allowed : 14.96 % 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: 1.42 (0.28), residues: 876 helix: 1.68 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -1.02 (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 B 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 0.00294 / 0.13 ( 7678) covalent geometry : angle 0.54836 / 0.28 (10420) SS BOND : bond 0.01353 / 0.68 ( 2) SS BOND : angle 2.80763 / 1.70 ( 4) hydrogen bonds : bond 0.04438 / 2.89 ( 486) hydrogen bonds : angle 3.82000 / 2.70 ( 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 127 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.259 Fit side-chains REVERT: A 61 PHE cc_start: 0.7714 (m-10) cc_final: 0.7277 (m-80) REVERT: A 68 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6968 (mm-30) REVERT: A 185 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.6956 (ttm-80) REVERT: A 213 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7266 (mmt180) REVERT: A 304 GLU cc_start: 0.7118 (pm20) cc_final: 0.6770 (mp0) REVERT: A 422 LEU cc_start: 0.8281 (tp) cc_final: 0.8068 (tp) REVERT: A 529 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9024 (mp) REVERT: B 70 ARG cc_start: 0.7150 (mtm-85) cc_final: 0.6940 (mpp80) REVERT: B 185 ARG cc_start: 0.7762 (ttp-170) cc_final: 0.7030 (ttm-80) REVERT: B 422 LEU cc_start: 0.8279 (tp) cc_final: 0.8063 (tp) REVERT: B 529 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9034 (mp) outliers start: 21 outliers final: 12 residues processed: 120 average time/residue: 0.4943 time to fit residues: 62.5894 Evaluate side-chains 113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 74 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 75 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.123771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.095293 restraints weight = 11875.277| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.48 r_work: 0.2785 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 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 = 0.2662 r_free = 0.2662 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: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1347 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= 0.122 Angle : 0.521 5.935 10424 Z= 0.270 Chirality : 0.038 0.126 1228 Planarity : 0.004 0.041 1202 Dihedral : 12.678 106.293 1552 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.56 % Allowed : 15.73 % Favored : 81.71 % 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: 1.99 (0.29), residues: 876 helix: 2.08 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.79 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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 285 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7678) covalent geometry : angle 0.51837 / 0.27 (10420) SS BOND : bond 0.01271 / 0.64 ( 2) SS BOND : angle 2.79312 / 1.69 ( 4) hydrogen bonds : bond 0.04164 / 2.71 ( 486) hydrogen bonds : angle 3.67720 / 2.60 ( 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 126 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.394 Fit side-chains REVERT: A 61 PHE cc_start: 0.7662 (m-10) cc_final: 0.7168 (m-80) REVERT: A 68 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6955 (mm-30) REVERT: A 70 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.7120 (ptp90) REVERT: A 185 ARG cc_start: 0.7824 (ttp-170) cc_final: 0.6940 (ttm-80) REVERT: A 304 GLU cc_start: 0.7087 (pm20) cc_final: 0.6756 (mp0) REVERT: A 422 LEU cc_start: 0.8279 (tp) cc_final: 0.8065 (tp) REVERT: A 478 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7693 (mtm180) REVERT: A 529 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9048 (mp) REVERT: B 185 ARG cc_start: 0.7776 (ttp-170) cc_final: 0.7030 (ttm-80) REVERT: B 422 LEU cc_start: 0.8282 (tp) cc_final: 0.8067 (tp) REVERT: B 529 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9060 (mp) outliers start: 18 outliers final: 8 residues processed: 118 average time/residue: 0.5256 time to fit residues: 65.6988 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 : 0.275 ------------------------------------------------------------------------------- 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 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 304 GLU 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: 0.0040 chunk 38 optimal weight: 0.0670 chunk 3 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.5130 ------------------------------------------------------------------------------- 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 = 0.3370 r_free = 0.3370 target = 0.125228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.098679 restraints weight = 8704.923| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.27 r_work: 0.2844 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1574 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= 0.102 Angle : 0.484 5.262 10424 Z= 0.253 Chirality : 0.037 0.121 1228 Planarity : 0.004 0.039 1202 Dihedral : 11.877 103.811 1546 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.17 % Allowed : 16.24 % 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: 2.36 (0.29), residues: 876 helix: 2.37 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.69 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 528 TYR 0.014 0.002 TYR B 195 PHE 0.013 0.001 PHE B 196 TRP 0.006 0.001 TRP A 285 HIS 0.002 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 7678) covalent geometry : angle 0.48148 / 0.25 (10420) SS BOND : bond 0.01219 / 0.61 ( 2) SS BOND : angle 2.69263 / 1.62 ( 4) hydrogen bonds : bond 0.03578 / 2.33 ( 486) hydrogen bonds : angle 3.54695 / 2.50 ( 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 122 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.278 Fit side-chains REVERT: A 61 PHE cc_start: 0.7505 (m-10) cc_final: 0.6928 (m-80) REVERT: A 68 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6968 (mm-30) REVERT: A 70 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.7070 (ptp90) REVERT: A 185 ARG cc_start: 0.7783 (ttp-170) cc_final: 0.6920 (ttm-80) REVERT: A 304 GLU cc_start: 0.7080 (pm20) cc_final: 0.6716 (mp0) REVERT: A 478 ARG cc_start: 0.8092 (mtp180) cc_final: 0.7657 (mtm180) REVERT: A 529 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9027 (mp) REVERT: B 65 SER cc_start: 0.7749 (m) cc_final: 0.7510 (p) REVERT: B 185 ARG cc_start: 0.7734 (ttp-170) cc_final: 0.7007 (ttm-80) REVERT: B 304 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6722 (pm20) REVERT: B 529 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9035 (mp) outliers start: 15 outliers final: 7 residues processed: 115 average time/residue: 0.5219 time to fit residues: 63.1985 Evaluate side-chains 113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 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 304 GLU 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: 0.7980 chunk 46 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 74 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.121987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.095196 restraints weight = 9196.640| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.31 r_work: 0.2818 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1482 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= 0.131 Angle : 0.530 5.363 10424 Z= 0.276 Chirality : 0.038 0.129 1228 Planarity : 0.004 0.038 1202 Dihedral : 11.990 103.823 1546 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.43 % Allowed : 15.73 % 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: 2.22 (0.29), residues: 876 helix: 2.23 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.64 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 528 TYR 0.016 0.002 TYR A 195 PHE 0.013 0.001 PHE B 196 TRP 0.006 0.001 TRP A 42 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 7678) covalent geometry : angle 0.52642 / 0.27 (10420) SS BOND : bond 0.01304 / 0.65 ( 2) SS BOND : angle 3.02636 / 1.81 ( 4) hydrogen bonds : bond 0.04264 / 2.77 ( 486) hydrogen bonds : angle 3.61182 / 2.55 ( 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 127 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.189 Fit side-chains REVERT: A 61 PHE cc_start: 0.7599 (m-10) cc_final: 0.7063 (m-80) REVERT: A 68 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7000 (mm-30) REVERT: A 70 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7176 (ptp90) REVERT: A 185 ARG cc_start: 0.7834 (ttp-170) cc_final: 0.6991 (ttm-80) REVERT: A 304 GLU cc_start: 0.7209 (pm20) cc_final: 0.6851 (mp0) REVERT: A 422 LEU cc_start: 0.8334 (tp) cc_final: 0.8115 (tp) REVERT: A 478 ARG cc_start: 0.8168 (mtp180) cc_final: 0.7721 (mtm180) REVERT: A 486 SER cc_start: 0.7488 (OUTLIER) cc_final: 0.7178 (p) REVERT: A 529 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9066 (mp) REVERT: B 65 SER cc_start: 0.7816 (m) cc_final: 0.7591 (p) REVERT: B 185 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7079 (ttm-80) REVERT: B 422 LEU cc_start: 0.8334 (tp) cc_final: 0.8121 (tp) REVERT: B 486 SER cc_start: 0.7431 (OUTLIER) cc_final: 0.7175 (p) REVERT: B 529 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9063 (mp) outliers start: 17 outliers final: 10 residues processed: 121 average time/residue: 0.5068 time to fit residues: 64.6652 Evaluate side-chains 119 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 0.0970 chunk 75 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3266 r_free = 0.3266 target = 0.117962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.088983 restraints weight = 10480.709| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.49 r_work: 0.2745 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7680 Z= 0.176 Angle : 0.598 5.531 10424 Z= 0.309 Chirality : 0.041 0.142 1228 Planarity : 0.005 0.043 1202 Dihedral : 12.143 104.284 1546 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.94 % Allowed : 15.60 % 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: 1.96 (0.28), residues: 876 helix: 2.05 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -0.76 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 528 TYR 0.017 0.002 TYR A 195 PHE 0.014 0.002 PHE B 196 TRP 0.007 0.001 TRP A 42 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 7678) covalent geometry : angle 0.59441 / 0.31 (10420) SS BOND : bond 0.01404 / 0.70 ( 2) SS BOND : angle 3.36586 / 2.00 ( 4) hydrogen bonds : bond 0.04986 / 3.24 ( 486) hydrogen bonds : angle 3.73637 / 2.64 ( 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 129 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.287 Fit side-chains REVERT: A 61 PHE cc_start: 0.7722 (m-10) cc_final: 0.7277 (m-80) REVERT: A 68 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6973 (mm-30) REVERT: A 70 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7165 (ptp90) REVERT: A 185 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.6963 (ttm-80) REVERT: A 304 GLU cc_start: 0.7152 (pm20) cc_final: 0.6756 (mp0) REVERT: A 478 ARG cc_start: 0.8175 (mtp180) cc_final: 0.7690 (mtm180) REVERT: A 529 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9013 (mp) REVERT: B 65 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7561 (p) REVERT: B 185 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.7052 (ttm-80) REVERT: B 294 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6540 (pmt170) REVERT: B 529 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9010 (mp) outliers start: 21 outliers final: 10 residues processed: 124 average time/residue: 0.4645 time to fit residues: 60.8966 Evaluate side-chains 120 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 65 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 294 ARG 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: 0.5980 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.122139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.094704 restraints weight = 8600.756| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.31 r_work: 0.2820 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1629 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= 0.111 Angle : 0.506 5.436 10424 Z= 0.265 Chirality : 0.038 0.153 1228 Planarity : 0.004 0.038 1202 Dihedral : 11.618 103.190 1546 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.81 % Allowed : 16.11 % Favored : 81.07 % 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: 2.29 (0.29), residues: 876 helix: 2.31 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.70 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 528 TYR 0.014 0.002 TYR B 195 PHE 0.013 0.001 PHE B 196 TRP 0.006 0.001 TRP A 285 HIS 0.002 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7678) covalent geometry : angle 0.50329 / 0.26 (10420) SS BOND : bond 0.01219 / 0.61 ( 2) SS BOND : angle 2.87170 / 1.72 ( 4) hydrogen bonds : bond 0.03795 / 2.47 ( 486) hydrogen bonds : angle 3.58394 / 2.52 ( 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 124 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.229 Fit side-chains REVERT: A 61 PHE cc_start: 0.7589 (m-10) cc_final: 0.7066 (m-80) REVERT: A 68 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6970 (mm-30) REVERT: A 70 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7148 (ptp90) REVERT: A 185 ARG cc_start: 0.7786 (ttp-170) cc_final: 0.6934 (ttm-80) REVERT: A 304 GLU cc_start: 0.7161 (pm20) cc_final: 0.6773 (mp0) REVERT: A 478 ARG cc_start: 0.8130 (mtp180) cc_final: 0.7670 (mtm180) REVERT: B 65 SER cc_start: 0.7782 (m) cc_final: 0.7572 (p) REVERT: B 185 ARG cc_start: 0.7763 (ttp-170) cc_final: 0.7031 (ttm-80) REVERT: B 486 SER cc_start: 0.7692 (OUTLIER) cc_final: 0.7272 (p) outliers start: 20 outliers final: 8 residues processed: 115 average time/residue: 0.4459 time to fit residues: 54.2056 Evaluate side-chains 112 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 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 304 GLU Chi-restraints excluded: chain B residue 486 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3325 r_free = 0.3325 target = 0.122094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.094953 restraints weight = 8209.515| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.28 r_work: 0.2825 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7680 Z= 0.112 Angle : 0.503 5.310 10424 Z= 0.263 Chirality : 0.038 0.138 1228 Planarity : 0.004 0.040 1202 Dihedral : 11.340 102.750 1546 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.92 % Allowed : 16.88 % Favored : 81.20 % 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: 2.36 (0.29), residues: 876 helix: 2.37 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.72 (0.40), residues: 240 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 285 HIS 0.002 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7678) covalent geometry : angle 0.49997 / 0.26 (10420) SS BOND : bond 0.01199 / 0.60 ( 2) SS BOND : angle 2.80909 / 1.68 ( 4) hydrogen bonds : bond 0.03843 / 2.50 ( 486) hydrogen bonds : angle 3.55346 / 2.50 ( 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 117 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.279 Fit side-chains REVERT: A 32 ARG cc_start: 0.7355 (mpt-90) cc_final: 0.6493 (mtp85) REVERT: A 61 PHE cc_start: 0.7531 (m-10) cc_final: 0.6964 (m-80) REVERT: A 68 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6959 (mm-30) REVERT: A 70 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.7089 (ptp90) REVERT: A 185 ARG cc_start: 0.7772 (ttp-170) cc_final: 0.6929 (ttm-80) REVERT: A 304 GLU cc_start: 0.7196 (pm20) cc_final: 0.6793 (mp0) REVERT: A 478 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7840 (mtm180) REVERT: B 65 SER cc_start: 0.7747 (OUTLIER) cc_final: 0.7541 (p) REVERT: B 185 ARG cc_start: 0.7750 (ttp-170) cc_final: 0.7027 (ttm-80) REVERT: B 295 GLU cc_start: 0.8118 (mp0) cc_final: 0.7829 (mp0) REVERT: B 486 SER cc_start: 0.7658 (OUTLIER) cc_final: 0.7279 (p) outliers start: 13 outliers final: 8 residues processed: 112 average time/residue: 0.5090 time to fit residues: 60.1684 Evaluate side-chains 113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 B residue 65 SER 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 304 GLU Chi-restraints excluded: chain B residue 486 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 38 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.120605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.093408 restraints weight = 7874.846| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.27 r_work: 0.2843 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 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 0.023 7680 Z= 0.128 Angle : 0.531 5.351 10424 Z= 0.277 Chirality : 0.039 0.142 1228 Planarity : 0.004 0.040 1202 Dihedral : 11.416 103.667 1546 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 2.24 (0.29), residues: 876 helix: 2.29 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 240 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 0.00288 / 0.13 ( 7678) covalent geometry : angle 0.52814 / 0.28 (10420) SS BOND : bond 0.01216 / 0.61 ( 2) SS BOND : angle 2.96183 / 1.76 ( 4) hydrogen bonds : bond 0.04157 / 2.71 ( 486) hydrogen bonds : angle 3.59906 / 2.53 ( 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 117 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.277 Fit side-chains REVERT: A 61 PHE cc_start: 0.7592 (m-10) cc_final: 0.7040 (m-80) REVERT: A 68 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6956 (mm-30) REVERT: A 70 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7141 (ptp90) REVERT: A 185 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.6969 (ttm-80) REVERT: A 304 GLU cc_start: 0.7217 (pm20) cc_final: 0.6828 (mp0) REVERT: A 478 ARG cc_start: 0.8130 (mtp180) cc_final: 0.7856 (mtm180) REVERT: B 65 SER cc_start: 0.7783 (OUTLIER) cc_final: 0.7569 (p) REVERT: B 185 ARG cc_start: 0.7774 (ttp-170) cc_final: 0.7061 (ttm-80) REVERT: B 295 GLU cc_start: 0.8132 (mp0) cc_final: 0.7860 (mp0) REVERT: B 486 SER cc_start: 0.7701 (OUTLIER) cc_final: 0.7499 (t) outliers start: 13 outliers final: 9 residues processed: 112 average time/residue: 0.4885 time to fit residues: 57.6163 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 : 0.202 ------------------------------------------------------------------------------- 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 300 ILE Chi-restraints excluded: chain B residue 65 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 80 optimal weight: 0.0570 chunk 71 optimal weight: 0.7980 chunk 78 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 0.0570 chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 0.0040 chunk 79 optimal weight: 0.9980 overall best weight: 0.2228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN A 421 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.125384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.098055 restraints weight = 9111.018| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.36 r_work: 0.2874 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7680 Z= 0.089 Angle : 0.462 5.183 10424 Z= 0.242 Chirality : 0.036 0.127 1228 Planarity : 0.004 0.037 1202 Dihedral : 10.934 101.826 1546 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.66 % Allowed : 17.14 % Favored : 81.20 % 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: 2.64 (0.29), residues: 876 helix: 2.62 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.73 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 528 TYR 0.012 0.001 TYR B 195 PHE 0.013 0.001 PHE B 196 TRP 0.008 0.001 TRP A 285 HIS 0.001 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.09 ( 7678) covalent geometry : angle 0.45982 / 0.24 (10420) SS BOND : bond 0.01112 / 0.56 ( 2) SS BOND : angle 2.53174 / 1.50 ( 4) hydrogen bonds : bond 0.03074 / 2.01 ( 486) hydrogen bonds : angle 3.48826 / 2.45 ( 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: 11 poor density : 104 time to evaluate : 0.208 Fit side-chains REVERT: A 32 ARG cc_start: 0.7298 (mpt-90) cc_final: 0.6435 (mtp85) REVERT: A 70 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.7064 (ptp90) REVERT: A 185 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.6892 (ttm-80) REVERT: A 304 GLU cc_start: 0.7137 (pm20) cc_final: 0.6686 (mp0) REVERT: A 478 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7744 (mtm180) REVERT: B 32 ARG cc_start: 0.7292 (mpt-90) cc_final: 0.6467 (mtp85) REVERT: B 65 SER cc_start: 0.7646 (OUTLIER) cc_final: 0.7442 (p) REVERT: B 185 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.6984 (ttm-80) REVERT: B 295 GLU cc_start: 0.8089 (mp0) cc_final: 0.7853 (mp0) REVERT: B 304 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6665 (pm20) outliers start: 11 outliers final: 6 residues processed: 108 average time/residue: 0.4763 time to fit residues: 54.1551 Evaluate side-chains 112 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL 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 65 SER 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 304 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.121766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.094558 restraints weight = 8386.787| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.30 r_work: 0.2823 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 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: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1710 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= 0.120 Angle : 0.512 5.325 10424 Z= 0.267 Chirality : 0.038 0.139 1228 Planarity : 0.004 0.038 1202 Dihedral : 11.084 102.916 1546 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.41 % Allowed : 16.88 % Favored : 81.71 % 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: 2.50 (0.29), residues: 876 helix: 2.49 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.70 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 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 A 499 HIS 0.002 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7678) covalent geometry : angle 0.50941 / 0.27 (10420) SS BOND : bond 0.01172 / 0.59 ( 2) SS BOND : angle 2.82703 / 1.68 ( 4) hydrogen bonds : bond 0.03940 / 2.56 ( 486) hydrogen bonds : angle 3.52244 / 2.48 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2922.67 seconds wall clock time: 50 minutes 24.86 seconds (3024.86 seconds total)