Starting phenix.real_space_refine on Thu Jul 2 00:11:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hnd_34911/07_2026/8hnd_34911.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnd_34911/07_2026/8hnd_34911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hnd_34911/07_2026/8hnd_34911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnd_34911/07_2026/8hnd_34911.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hnd_34911/07_2026/8hnd_34911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnd_34911/07_2026/8hnd_34911.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hnd_34911/07_2026/8hnd_34911.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hnd_34911/07_2026/8hnd_34911.cif" } resolution = 3.19 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= 0.002 sd= 0.122 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 2879 2.51 5 N 685 2.21 5 O 770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 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: 4370 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4304 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 19, 'TRANS': 540} Chain breaks: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 3, 'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'FY5': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.09, per 1000 atoms: 0.25 Number of scatterers: 4370 At special positions: 0 Unit cell: (56.852, 68.036, 103.452, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 770 8.00 N 685 7.00 C 2879 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.02 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.02 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 802 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 158.1 milliseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1018 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 67.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 27 through 50 removed outlier: 4.176A pdb=" N LEU A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 removed outlier: 3.641A pdb=" N ARG A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 86 removed outlier: 4.090A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.817A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 204 through 217 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 258 through 274 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 335 through 367 removed outlier: 4.766A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 381 removed outlier: 3.622A pdb=" N ALA A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.728A pdb=" N ILE A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 423 removed outlier: 3.538A pdb=" N LYS A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.742A pdb=" N LEU A 512 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 513 " --> pdb=" O THR A 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 513' Processing helix chain 'A' and resid 527 through 550 removed outlier: 3.948A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 562 removed outlier: 3.507A pdb=" N HIS A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 567 through 598 Proline residue: A 588 - end of helix Processing helix chain 'A' and resid 617 through 651 Processing sheet with id=AA1, first strand: chain 'A' and resid 473 through 475 removed outlier: 3.870A pdb=" N SER A 491 " --> pdb=" O TYR A 502 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 599 through 604 removed outlier: 6.984A pdb=" N CYS A 599 " --> pdb=" O TYR A 616 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR A 616 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS A 601 " --> pdb=" O ARG A 614 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A 612 " --> pdb=" O SER A 603 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 813 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: 0.66 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 669 1.32 - 1.44: 1283 1.44 - 1.57: 2474 1.57 - 1.69: 1 1.69 - 1.81: 52 Bond restraints: 4479 Sorted by residual: bond pdb=" CA LEU A 27 " pdb=" C LEU A 27 " ideal model delta sigma weight residual 1.530 1.473 0.057 1.11e-02 8.12e+03 2.60e+01 bond pdb=" C SER A 630 " pdb=" O SER A 630 " ideal model delta sigma weight residual 1.237 1.196 0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" O22 FY5 A 801 " pdb=" S21 FY5 A 801 " ideal model delta sigma weight residual 1.461 1.527 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" O20 FY5 A 801 " pdb=" S21 FY5 A 801 " ideal model delta sigma weight residual 1.673 1.613 0.060 2.00e-02 2.50e+03 8.98e+00 bond pdb=" O23 FY5 A 801 " pdb=" S21 FY5 A 801 " ideal model delta sigma weight residual 1.458 1.399 0.059 2.00e-02 2.50e+03 8.70e+00 ... (remaining 4474 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 5686 2.18 - 4.36: 307 4.36 - 6.54: 44 6.54 - 8.72: 20 8.72 - 10.90: 16 Bond angle restraints: 6073 Sorted by residual: angle pdb=" N LYS A 28 " pdb=" CA LYS A 28 " pdb=" C LYS A 28 " ideal model delta sigma weight residual 113.41 103.39 10.02 1.22e+00 6.72e-01 6.74e+01 angle pdb=" N GLN A 369 " pdb=" CA GLN A 369 " pdb=" C GLN A 369 " ideal model delta sigma weight residual 109.64 118.36 -8.72 1.27e+00 6.20e-01 4.72e+01 angle pdb=" N GLU A 523 " pdb=" CA GLU A 523 " pdb=" C GLU A 523 " ideal model delta sigma weight residual 110.59 100.77 9.82 1.45e+00 4.76e-01 4.58e+01 angle pdb=" C PHE A 278 " pdb=" CA PHE A 278 " pdb=" CB PHE A 278 " ideal model delta sigma weight residual 111.51 101.08 10.43 1.58e+00 4.01e-01 4.36e+01 angle pdb=" N GLU A 60 " pdb=" CA GLU A 60 " pdb=" C GLU A 60 " ideal model delta sigma weight residual 111.52 120.47 -8.95 1.40e+00 5.10e-01 4.09e+01 ... (remaining 6068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 2371 17.72 - 35.45: 168 35.45 - 53.17: 32 53.17 - 70.89: 5 70.89 - 88.61: 2 Dihedral angle restraints: 2578 sinusoidal: 975 harmonic: 1603 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -159.05 73.05 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 524 " pdb=" CB CYS A 524 " ideal model delta sinusoidal sigma weight residual 93.00 39.59 53.41 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" C CYS A 506 " pdb=" N CYS A 506 " pdb=" CA CYS A 506 " pdb=" CB CYS A 506 " ideal model delta harmonic sigma weight residual -122.60 -108.76 -13.84 0 2.50e+00 1.60e-01 3.07e+01 ... (remaining 2575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 668 0.126 - 0.252: 26 0.252 - 0.378: 7 0.378 - 0.504: 1 0.504 - 0.630: 3 Chirality restraints: 705 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 3.98e+01 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 516 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -3.03 0.63 2.00e-01 2.50e+01 9.93e+00 chirality pdb=" CA GLU A 60 " pdb=" N GLU A 60 " pdb=" C GLU A 60 " pdb=" CB GLU A 60 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.75e+00 ... (remaining 702 not shown) Planarity restraints: 737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.356 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG B 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.130 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " 0.300 2.00e-02 2.50e+03 2.54e-01 8.06e+02 pdb=" C7 NAG A 802 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " -0.438 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.291 2.00e-02 2.50e+03 2.45e-01 7.53e+02 pdb=" C7 NAG B 2 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.420 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.022 2.00e-02 2.50e+03 ... (remaining 734 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1062 2.76 - 3.30: 4596 3.30 - 3.83: 7270 3.83 - 4.37: 8863 4.37 - 4.90: 14390 Nonbonded interactions: 36181 Sorted by model distance: nonbonded pdb=" O ILE A 595 " pdb=" OG1 THR A 598 " model vdw 2.231 3.040 nonbonded pdb=" NE2 GLN A 541 " pdb=" O23 FY5 A 801 " model vdw 2.370 3.120 nonbonded pdb=" O THR A 609 " pdb=" C ARG A 610 " model vdw 2.380 3.270 nonbonded pdb=" N GLU A 523 " pdb=" O GLU A 523 " model vdw 2.421 2.496 nonbonded pdb=" OD1 ASN A 432 " pdb=" OG1 THR A 619 " model vdw 2.423 3.040 ... (remaining 36176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 : 0.008 0.075 4489 Z= 0.523 Angle : 1.265 18.319 6096 Z= 0.810 Chirality : 0.074 0.630 705 Planarity : 0.018 0.306 735 Dihedral : 12.210 88.611 1539 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.65 % Allowed : 5.17 % Favored : 94.18 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.30), residues: 552 helix: -0.97 (0.25), residues: 351 sheet: None (None), residues: 0 loop : -3.32 (0.32), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 253 TYR 0.019 0.001 TYR A 590 PHE 0.012 0.001 PHE A 117 TRP 0.008 0.001 TRP A 259 HIS 0.006 0.002 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.52 ( 4479) covalent geometry : angle 1.22102 / 0.80 ( 6073) SS BOND : bond 0.00396 / 0.26 ( 7) SS BOND : angle 1.29125 / 0.74 ( 14) hydrogen bonds : bond 0.18574 / 12.98 ( 276) hydrogen bonds : angle 8.18257 / 5.84 ( 813) link_BETA1-4 : bond 0.00335 / 0.21 ( 1) link_BETA1-4 : angle 0.87468 / 0.38 ( 3) link_NAG-ASN : bond 0.05316 / 2.95 ( 2) link_NAG-ASN : angle 10.62400 / 6.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 38 PHE cc_start: 0.6995 (m-80) cc_final: 0.6754 (m-80) REVERT: A 48 MET cc_start: 0.7698 (tpt) cc_final: 0.7447 (tpt) REVERT: A 86 TYR cc_start: 0.6727 (t80) cc_final: 0.6460 (t80) REVERT: A 568 LYS cc_start: 0.7704 (tttt) cc_final: 0.6777 (tptt) REVERT: A 640 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7549 (t80) outliers start: 3 outliers final: 0 residues processed: 100 average time/residue: 0.0630 time to fit residues: 8.2447 Evaluate side-chains 76 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 541 GLN A 606 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.178835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.137146 restraints weight = 4805.661| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.82 r_work: 0.3305 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4489 Z= 0.172 Angle : 0.746 13.583 6096 Z= 0.353 Chirality : 0.044 0.230 705 Planarity : 0.005 0.033 735 Dihedral : 5.742 72.019 608 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.23 % Allowed : 11.64 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.34), residues: 552 helix: 0.73 (0.26), residues: 359 sheet: None (None), residues: 0 loop : -2.32 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 93 TYR 0.022 0.002 TYR A 338 PHE 0.022 0.002 PHE A 341 TRP 0.006 0.001 TRP A 259 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 4479) covalent geometry : angle 0.73631 / 0.35 ( 6073) SS BOND : bond 0.00343 / 0.24 ( 7) SS BOND : angle 1.33723 / 0.70 ( 14) hydrogen bonds : bond 0.05063 / 3.39 ( 276) hydrogen bonds : angle 5.16382 / 3.69 ( 813) link_BETA1-4 : bond 0.00598 / 0.37 ( 1) link_BETA1-4 : angle 0.72249 / 0.34 ( 3) link_NAG-ASN : bond 0.00612 / 0.38 ( 2) link_NAG-ASN : angle 3.57226 / 2.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.7453 (tpt) cc_final: 0.7250 (tpt) REVERT: A 118 MET cc_start: 0.8585 (ttm) cc_final: 0.8169 (mtp) REVERT: A 640 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7248 (t80) REVERT: A 649 LYS cc_start: 0.7707 (tptt) cc_final: 0.6496 (mmtm) outliers start: 15 outliers final: 8 residues processed: 87 average time/residue: 0.0380 time to fit residues: 4.4711 Evaluate side-chains 78 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 34 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.176341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134259 restraints weight = 4783.462| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.86 r_work: 0.3313 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4489 Z= 0.152 Angle : 0.643 9.229 6096 Z= 0.310 Chirality : 0.041 0.155 705 Planarity : 0.004 0.036 735 Dihedral : 5.673 74.936 608 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.23 % Allowed : 14.66 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.35), residues: 552 helix: 1.20 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -1.91 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 526 TYR 0.020 0.002 TYR A 590 PHE 0.020 0.001 PHE A 73 TRP 0.004 0.001 TRP A 259 HIS 0.004 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 4479) covalent geometry : angle 0.63464 / 0.31 ( 6073) SS BOND : bond 0.00219 / 0.13 ( 7) SS BOND : angle 1.12146 / 0.61 ( 14) hydrogen bonds : bond 0.04492 / 3.04 ( 276) hydrogen bonds : angle 4.81796 / 3.45 ( 813) link_BETA1-4 : bond 0.00101 / 0.06 ( 1) link_BETA1-4 : angle 0.63971 / 0.25 ( 3) link_NAG-ASN : bond 0.00283 / 0.17 ( 2) link_NAG-ASN : angle 2.93949 / 1.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 623 ARG cc_start: 0.7334 (ttt90) cc_final: 0.6083 (ttp-170) REVERT: A 640 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7338 (t80) outliers start: 15 outliers final: 9 residues processed: 91 average time/residue: 0.0645 time to fit residues: 7.7617 Evaluate side-chains 80 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.169884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.129349 restraints weight = 4708.908| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.78 r_work: 0.3194 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4489 Z= 0.168 Angle : 0.639 14.338 6096 Z= 0.304 Chirality : 0.041 0.159 705 Planarity : 0.004 0.039 735 Dihedral : 5.589 74.127 608 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.23 % Allowed : 16.81 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.35), residues: 552 helix: 1.39 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.70 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 614 TYR 0.021 0.002 TYR A 590 PHE 0.018 0.001 PHE A 175 TRP 0.004 0.001 TRP A 259 HIS 0.007 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 4479) covalent geometry : angle 0.63186 / 0.30 ( 6073) SS BOND : bond 0.00241 / 0.15 ( 7) SS BOND : angle 1.28799 / 0.61 ( 14) hydrogen bonds : bond 0.04473 / 3.03 ( 276) hydrogen bonds : angle 4.74929 / 3.41 ( 813) link_BETA1-4 : bond 0.00250 / 0.16 ( 1) link_BETA1-4 : angle 0.35338 / 0.17 ( 3) link_NAG-ASN : bond 0.00225 / 0.13 ( 2) link_NAG-ASN : angle 2.50549 / 1.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 517 TYR cc_start: 0.5419 (m-80) cc_final: 0.5124 (m-10) REVERT: A 623 ARG cc_start: 0.7133 (ttt90) cc_final: 0.5809 (ttp-170) REVERT: A 640 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.7075 (t80) outliers start: 15 outliers final: 10 residues processed: 85 average time/residue: 0.0512 time to fit residues: 5.9508 Evaluate side-chains 82 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.171136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130600 restraints weight = 4747.047| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.79 r_work: 0.3311 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4489 Z= 0.148 Angle : 0.607 12.199 6096 Z= 0.293 Chirality : 0.040 0.143 705 Planarity : 0.004 0.039 735 Dihedral : 5.521 73.396 608 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.45 % Allowed : 18.53 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.35), residues: 552 helix: 1.65 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -1.56 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 633 TYR 0.020 0.001 TYR A 590 PHE 0.017 0.001 PHE A 175 TRP 0.005 0.001 TRP A 259 HIS 0.005 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 4479) covalent geometry : angle 0.60174 / 0.29 ( 6073) SS BOND : bond 0.00207 / 0.12 ( 7) SS BOND : angle 1.05577 / 0.53 ( 14) hydrogen bonds : bond 0.04289 / 2.91 ( 276) hydrogen bonds : angle 4.66440 / 3.37 ( 813) link_BETA1-4 : bond 0.00283 / 0.18 ( 1) link_BETA1-4 : angle 0.45140 / 0.19 ( 3) link_NAG-ASN : bond 0.00248 / 0.14 ( 2) link_NAG-ASN : angle 2.26717 / 1.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8600 (mtp) cc_final: 0.8075 (mtp) REVERT: A 517 TYR cc_start: 0.5796 (m-80) cc_final: 0.5126 (m-10) REVERT: A 623 ARG cc_start: 0.7336 (ttt90) cc_final: 0.6105 (ttp-170) REVERT: A 640 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7406 (t80) outliers start: 16 outliers final: 13 residues processed: 88 average time/residue: 0.0544 time to fit residues: 6.5984 Evaluate side-chains 83 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.0070 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.175396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132318 restraints weight = 4865.784| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.91 r_work: 0.3288 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4489 Z= 0.156 Angle : 0.609 12.073 6096 Z= 0.296 Chirality : 0.041 0.141 705 Planarity : 0.004 0.039 735 Dihedral : 5.475 72.539 608 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.45 % Allowed : 18.75 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.35), residues: 552 helix: 1.75 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -1.51 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 614 TYR 0.020 0.001 TYR A 590 PHE 0.018 0.001 PHE A 175 TRP 0.005 0.001 TRP A 602 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 4479) covalent geometry : angle 0.60388 / 0.29 ( 6073) SS BOND : bond 0.00224 / 0.14 ( 7) SS BOND : angle 1.06853 / 0.53 ( 14) hydrogen bonds : bond 0.04290 / 2.88 ( 276) hydrogen bonds : angle 4.66697 / 3.40 ( 813) link_BETA1-4 : bond 0.00260 / 0.16 ( 1) link_BETA1-4 : angle 0.31883 / 0.15 ( 3) link_NAG-ASN : bond 0.00217 / 0.13 ( 2) link_NAG-ASN : angle 2.11989 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.7414 (mmt) cc_final: 0.7182 (mmt) REVERT: A 517 TYR cc_start: 0.5786 (m-80) cc_final: 0.5164 (m-10) REVERT: A 623 ARG cc_start: 0.7322 (ttt90) cc_final: 0.6114 (ttp-170) REVERT: A 640 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7402 (t80) outliers start: 16 outliers final: 13 residues processed: 84 average time/residue: 0.0547 time to fit residues: 6.1583 Evaluate side-chains 84 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.175265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.132311 restraints weight = 4859.107| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.94 r_work: 0.3286 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 4489 Z= 0.152 Angle : 0.593 11.446 6096 Z= 0.291 Chirality : 0.041 0.150 705 Planarity : 0.004 0.039 735 Dihedral : 5.450 71.895 608 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.88 % Allowed : 18.97 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.36), residues: 552 helix: 1.83 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.46 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 633 TYR 0.020 0.001 TYR A 590 PHE 0.017 0.001 PHE A 175 TRP 0.004 0.001 TRP A 602 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 4479) covalent geometry : angle 0.58789 / 0.29 ( 6073) SS BOND : bond 0.00247 / 0.14 ( 7) SS BOND : angle 1.14424 / 0.63 ( 14) hydrogen bonds : bond 0.04247 / 2.85 ( 276) hydrogen bonds : angle 4.64890 / 3.39 ( 813) link_BETA1-4 : bond 0.00122 / 0.08 ( 1) link_BETA1-4 : angle 0.19692 / 0.10 ( 3) link_NAG-ASN : bond 0.00214 / 0.12 ( 2) link_NAG-ASN : angle 1.99568 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 TYR cc_start: 0.5832 (m-80) cc_final: 0.5238 (m-10) REVERT: A 557 MET cc_start: 0.7893 (ttm) cc_final: 0.7610 (mtp) REVERT: A 623 ARG cc_start: 0.7363 (ttt90) cc_final: 0.6084 (ttt180) REVERT: A 640 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7441 (t80) outliers start: 18 outliers final: 16 residues processed: 87 average time/residue: 0.0405 time to fit residues: 4.8044 Evaluate side-chains 88 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 46 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 42 optimal weight: 0.0870 chunk 18 optimal weight: 0.0970 overall best weight: 0.3156 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.179139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.136246 restraints weight = 4774.401| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.94 r_work: 0.3334 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4489 Z= 0.115 Angle : 0.550 7.344 6096 Z= 0.278 Chirality : 0.039 0.150 705 Planarity : 0.004 0.038 735 Dihedral : 5.348 70.361 608 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.80 % Allowed : 20.26 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.36), residues: 552 helix: 1.98 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.29 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 93 TYR 0.018 0.001 TYR A 338 PHE 0.016 0.001 PHE A 175 TRP 0.006 0.001 TRP A 259 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 4479) covalent geometry : angle 0.54682 / 0.28 ( 6073) SS BOND : bond 0.00247 / 0.16 ( 7) SS BOND : angle 0.73337 / 0.40 ( 14) hydrogen bonds : bond 0.03842 / 2.58 ( 276) hydrogen bonds : angle 4.50721 / 3.29 ( 813) link_BETA1-4 : bond 0.00203 / 0.13 ( 1) link_BETA1-4 : angle 0.30676 / 0.15 ( 3) link_NAG-ASN : bond 0.00253 / 0.15 ( 2) link_NAG-ASN : angle 1.81180 / 1.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8232 (mtpp) REVERT: A 517 TYR cc_start: 0.5610 (m-80) cc_final: 0.5014 (m-10) REVERT: A 557 MET cc_start: 0.7784 (ttm) cc_final: 0.7498 (mtp) REVERT: A 623 ARG cc_start: 0.7396 (ttt90) cc_final: 0.6120 (ttt180) REVERT: A 640 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7379 (t80) outliers start: 13 outliers final: 9 residues processed: 86 average time/residue: 0.0598 time to fit residues: 6.7128 Evaluate side-chains 83 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.177940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.135003 restraints weight = 4752.329| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.92 r_work: 0.3312 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4489 Z= 0.132 Angle : 0.557 7.224 6096 Z= 0.283 Chirality : 0.040 0.152 705 Planarity : 0.004 0.037 735 Dihedral : 5.301 69.918 608 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.45 % Allowed : 20.04 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.36), residues: 552 helix: 2.01 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.19 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 526 TYR 0.019 0.001 TYR A 590 PHE 0.017 0.001 PHE A 102 TRP 0.004 0.001 TRP A 259 HIS 0.002 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 4479) covalent geometry : angle 0.55339 / 0.28 ( 6073) SS BOND : bond 0.00170 / 0.10 ( 7) SS BOND : angle 0.89605 / 0.49 ( 14) hydrogen bonds : bond 0.03916 / 2.63 ( 276) hydrogen bonds : angle 4.52806 / 3.31 ( 813) link_BETA1-4 : bond 0.00254 / 0.16 ( 1) link_BETA1-4 : angle 0.28261 / 0.15 ( 3) link_NAG-ASN : bond 0.00197 / 0.11 ( 2) link_NAG-ASN : angle 1.72529 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6830 (mt) REVERT: A 517 TYR cc_start: 0.5715 (m-80) cc_final: 0.5124 (m-10) REVERT: A 557 MET cc_start: 0.7756 (ttm) cc_final: 0.7483 (mtp) REVERT: A 623 ARG cc_start: 0.7369 (ttt90) cc_final: 0.6099 (ttt180) REVERT: A 640 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7259 (t80) outliers start: 16 outliers final: 13 residues processed: 81 average time/residue: 0.0509 time to fit residues: 5.6321 Evaluate side-chains 86 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 0.0070 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.173977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130050 restraints weight = 4765.815| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.96 r_work: 0.3216 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4489 Z= 0.130 Angle : 0.557 7.219 6096 Z= 0.284 Chirality : 0.040 0.157 705 Planarity : 0.004 0.037 735 Dihedral : 5.264 69.514 608 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.45 % Allowed : 19.83 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.36), residues: 552 helix: 2.03 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.17 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 526 TYR 0.019 0.001 TYR A 590 PHE 0.019 0.001 PHE A 102 TRP 0.004 0.001 TRP A 259 HIS 0.002 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 4479) covalent geometry : angle 0.55428 / 0.28 ( 6073) SS BOND : bond 0.00190 / 0.11 ( 7) SS BOND : angle 0.86360 / 0.47 ( 14) hydrogen bonds : bond 0.03907 / 2.61 ( 276) hydrogen bonds : angle 4.50703 / 3.29 ( 813) link_BETA1-4 : bond 0.00182 / 0.11 ( 1) link_BETA1-4 : angle 0.31104 / 0.16 ( 3) link_NAG-ASN : bond 0.00197 / 0.11 ( 2) link_NAG-ASN : angle 1.65877 / 0.96 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LYS cc_start: 0.8249 (ttmt) cc_final: 0.7916 (mtpp) REVERT: A 517 TYR cc_start: 0.5467 (m-80) cc_final: 0.4900 (m-10) REVERT: A 623 ARG cc_start: 0.7073 (ttt90) cc_final: 0.5829 (ttt180) REVERT: A 640 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.6938 (t80) outliers start: 16 outliers final: 14 residues processed: 81 average time/residue: 0.0547 time to fit residues: 6.0507 Evaluate side-chains 84 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 50 optimal weight: 0.0070 chunk 31 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 0.0040 chunk 4 optimal weight: 0.9990 overall best weight: 0.3810 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.175482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.134503 restraints weight = 4808.978| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.86 r_work: 0.3304 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 4489 Z= 0.114 Angle : 0.539 7.253 6096 Z= 0.275 Chirality : 0.039 0.160 705 Planarity : 0.004 0.036 735 Dihedral : 5.203 68.525 608 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.23 % Allowed : 20.26 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.37), residues: 552 helix: 1.95 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.90 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 253 TYR 0.018 0.001 TYR A 590 PHE 0.021 0.001 PHE A 102 TRP 0.006 0.001 TRP A 259 HIS 0.002 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 4479) covalent geometry : angle 0.53647 / 0.27 ( 6073) SS BOND : bond 0.00185 / 0.11 ( 7) SS BOND : angle 0.81525 / 0.46 ( 14) hydrogen bonds : bond 0.03726 / 2.50 ( 276) hydrogen bonds : angle 4.43522 / 3.25 ( 813) link_BETA1-4 : bond 0.00187 / 0.12 ( 1) link_BETA1-4 : angle 0.34344 / 0.18 ( 3) link_NAG-ASN : bond 0.00210 / 0.12 ( 2) link_NAG-ASN : angle 1.52584 / 0.89 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1066.07 seconds wall clock time: 19 minutes 0.83 seconds (1140.83 seconds total)