Starting phenix.real_space_refine on Tue Mar 3 12:46:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnd_34911/03_2026/8hnd_34911.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnd_34911/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hnd_34911/03_2026/8hnd_34911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnd_34911/03_2026/8hnd_34911.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnd_34911/03_2026/8hnd_34911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnd_34911/03_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.17, per 1000 atoms: 0.27 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: 0.36 Conformation dependent library (CDL) restraints added in 309.2 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: 0.10 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: 0.80 Time building geometry restraints manager: 0.49 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 - 20.85: 2488 20.85 - 41.69: 154 41.69 - 62.54: 24 62.54 - 83.38: 1 83.38 - 104.23: 9 Dihedral angle restraints: 2676 sinusoidal: 1073 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 2673 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: 1.060 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.460 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 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 : 14.366 104.227 1637 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 covalent geometry : bond 0.00758 ( 4479) covalent geometry : angle 1.22102 ( 6073) SS BOND : bond 0.00396 ( 7) SS BOND : angle 1.29125 ( 14) hydrogen bonds : bond 0.18574 ( 276) hydrogen bonds : angle 8.18257 ( 813) link_BETA1-4 : bond 0.00335 ( 1) link_BETA1-4 : angle 0.87468 ( 3) link_NAG-ASN : bond 0.05316 ( 2) link_NAG-ASN : angle 10.62400 ( 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 : 0.107 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: 0.0639 time to fit residues: 8.2384 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 : 0.155 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 178 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 606 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.179140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.136964 restraints weight = 4846.143| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.90 r_work: 0.3305 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4489 Z= 0.174 Angle : 0.737 13.514 6096 Z= 0.350 Chirality : 0.043 0.235 705 Planarity : 0.005 0.033 735 Dihedral : 8.874 73.149 706 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.45 % Allowed : 11.42 % 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 : -2.33 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 633 TYR 0.017 0.002 TYR A 338 PHE 0.022 0.001 PHE A 341 TRP 0.006 0.001 TRP A 259 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 4479) covalent geometry : angle 0.72614 ( 6073) SS BOND : bond 0.00301 ( 7) SS BOND : angle 1.27010 ( 14) hydrogen bonds : bond 0.05042 ( 276) hydrogen bonds : angle 5.14191 ( 813) link_BETA1-4 : bond 0.01134 ( 1) link_BETA1-4 : angle 1.00748 ( 3) link_NAG-ASN : bond 0.00532 ( 2) link_NAG-ASN : angle 3.71436 ( 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 95 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.7552 (tpt) cc_final: 0.7345 (tpt) REVERT: A 170 MET cc_start: 0.7792 (mmt) cc_final: 0.7586 (tpp) REVERT: A 640 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7348 (t80) REVERT: A 649 LYS cc_start: 0.7734 (tptt) cc_final: 0.6523 (mmtm) outliers start: 16 outliers final: 8 residues processed: 89 average time/residue: 0.0543 time to fit residues: 6.5400 Evaluate side-chains 80 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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: 0.9990 chunk 42 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 39 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3968 r_free = 0.3968 target = 0.178551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134450 restraints weight = 4791.939| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.13 r_work: 0.3279 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4489 Z= 0.128 Angle : 0.615 9.377 6096 Z= 0.297 Chirality : 0.040 0.169 705 Planarity : 0.004 0.034 735 Dihedral : 7.069 73.444 706 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.02 % Allowed : 14.66 % Favored : 82.33 % 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: 0.27 (0.35), residues: 552 helix: 1.23 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -1.89 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 633 TYR 0.019 0.001 TYR A 590 PHE 0.018 0.001 PHE A 73 TRP 0.004 0.001 TRP A 259 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4479) covalent geometry : angle 0.60577 ( 6073) SS BOND : bond 0.00224 ( 7) SS BOND : angle 1.07433 ( 14) hydrogen bonds : bond 0.04303 ( 276) hydrogen bonds : angle 4.74272 ( 813) link_BETA1-4 : bond 0.00413 ( 1) link_BETA1-4 : angle 1.45952 ( 3) link_NAG-ASN : bond 0.00245 ( 2) link_NAG-ASN : angle 2.92125 ( 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 91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 38 PHE cc_start: 0.5898 (m-80) cc_final: 0.5517 (m-80) REVERT: A 118 MET cc_start: 0.8590 (ttm) cc_final: 0.7966 (mtp) REVERT: A 623 ARG cc_start: 0.7112 (ttt90) cc_final: 0.5880 (ttp-170) REVERT: A 640 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7136 (t80) outliers start: 14 outliers final: 9 residues processed: 86 average time/residue: 0.0607 time to fit residues: 6.8631 Evaluate side-chains 81 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.093 ------------------------------------------------------------------------------- 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: 1.9990 chunk 40 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.176194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.132130 restraints weight = 4757.060| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.09 r_work: 0.3247 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4489 Z= 0.147 Angle : 0.607 12.692 6096 Z= 0.292 Chirality : 0.039 0.159 705 Planarity : 0.004 0.037 735 Dihedral : 6.850 72.322 706 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.59 % Allowed : 18.32 % Favored : 79.09 % 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: 0.61 (0.35), residues: 552 helix: 1.46 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.65 (0.41), residues: 194 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 0.016 0.001 PHE A 175 TRP 0.003 0.001 TRP A 259 HIS 0.002 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4479) covalent geometry : angle 0.59969 ( 6073) SS BOND : bond 0.00282 ( 7) SS BOND : angle 1.24156 ( 14) hydrogen bonds : bond 0.04249 ( 276) hydrogen bonds : angle 4.66603 ( 813) link_BETA1-4 : bond 0.00458 ( 1) link_BETA1-4 : angle 0.82484 ( 3) link_NAG-ASN : bond 0.00239 ( 2) link_NAG-ASN : angle 2.52520 ( 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 90 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 517 TYR cc_start: 0.5440 (m-80) cc_final: 0.5131 (m-10) REVERT: A 623 ARG cc_start: 0.7064 (ttt90) cc_final: 0.5770 (ttp-170) REVERT: A 640 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7145 (t80) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.0546 time to fit residues: 6.4374 Evaluate side-chains 84 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 51 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.0010 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.179136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134177 restraints weight = 4805.888| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.14 r_work: 0.3293 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 4489 Z= 0.144 Angle : 0.591 11.427 6096 Z= 0.287 Chirality : 0.040 0.143 705 Planarity : 0.004 0.038 735 Dihedral : 6.822 71.812 706 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.23 % Allowed : 18.10 % Favored : 78.66 % 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: 0.84 (0.35), residues: 552 helix: 1.61 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.52 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 633 TYR 0.019 0.001 TYR A 590 PHE 0.017 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 covalent geometry : bond 0.00345 ( 4479) covalent geometry : angle 0.58498 ( 6073) SS BOND : bond 0.00217 ( 7) SS BOND : angle 1.04023 ( 14) hydrogen bonds : bond 0.04197 ( 276) hydrogen bonds : angle 4.64103 ( 813) link_BETA1-4 : bond 0.00463 ( 1) link_BETA1-4 : angle 0.78247 ( 3) link_NAG-ASN : bond 0.00235 ( 2) link_NAG-ASN : angle 2.30394 ( 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 92 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8625 (mtp) cc_final: 0.8216 (mtp) REVERT: A 517 TYR cc_start: 0.6079 (m-80) cc_final: 0.5397 (m-10) REVERT: A 602 TRP cc_start: 0.8825 (m100) cc_final: 0.8571 (m100) REVERT: A 623 ARG cc_start: 0.7628 (ttt90) cc_final: 0.6432 (ttp-170) REVERT: A 640 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7733 (t80) outliers start: 15 outliers final: 12 residues processed: 88 average time/residue: 0.0546 time to fit residues: 6.4560 Evaluate side-chains 86 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 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 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 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 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: 7.9990 chunk 11 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3939 r_free = 0.3939 target = 0.175595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130433 restraints weight = 4891.439| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.13 r_work: 0.3178 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 4489 Z= 0.196 Angle : 0.628 13.161 6096 Z= 0.308 Chirality : 0.041 0.156 705 Planarity : 0.004 0.039 735 Dihedral : 6.950 71.456 706 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.56 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: 0.85 (0.35), residues: 552 helix: 1.70 (0.27), residues: 352 sheet: None (None), residues: 0 loop : -1.57 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 614 TYR 0.022 0.002 TYR A 590 PHE 0.020 0.001 PHE A 175 TRP 0.003 0.001 TRP A 259 HIS 0.005 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 4479) covalent geometry : angle 0.62293 ( 6073) SS BOND : bond 0.00313 ( 7) SS BOND : angle 1.25188 ( 14) hydrogen bonds : bond 0.04552 ( 276) hydrogen bonds : angle 4.75409 ( 813) link_BETA1-4 : bond 0.00437 ( 1) link_BETA1-4 : angle 0.73456 ( 3) link_NAG-ASN : bond 0.00175 ( 2) link_NAG-ASN : angle 2.15529 ( 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 : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8323 (mtp) cc_final: 0.7806 (mtp) REVERT: A 517 TYR cc_start: 0.5531 (m-80) cc_final: 0.4913 (m-10) REVERT: A 623 ARG cc_start: 0.7114 (ttt90) cc_final: 0.5896 (ttp-170) REVERT: A 640 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7211 (t80) outliers start: 16 outliers final: 10 residues processed: 83 average time/residue: 0.0566 time to fit residues: 6.3490 Evaluate side-chains 78 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 218 ILE Chi-restraints excluded: chain A residue 377 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: 0.6980 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.176511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131833 restraints weight = 4826.856| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.16 r_work: 0.3193 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 4489 Z= 0.130 Angle : 0.570 10.422 6096 Z= 0.283 Chirality : 0.039 0.131 705 Planarity : 0.004 0.037 735 Dihedral : 6.916 70.172 706 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.23 % Allowed : 19.40 % Favored : 77.37 % 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: 1.12 (0.36), residues: 552 helix: 1.88 (0.27), residues: 353 sheet: None (None), residues: 0 loop : -1.44 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 633 TYR 0.022 0.001 TYR A 338 PHE 0.017 0.001 PHE A 175 TRP 0.005 0.001 TRP A 259 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4479) covalent geometry : angle 0.56522 ( 6073) SS BOND : bond 0.00243 ( 7) SS BOND : angle 1.06064 ( 14) hydrogen bonds : bond 0.04068 ( 276) hydrogen bonds : angle 4.60588 ( 813) link_BETA1-4 : bond 0.00452 ( 1) link_BETA1-4 : angle 0.82171 ( 3) link_NAG-ASN : bond 0.00252 ( 2) link_NAG-ASN : angle 1.97455 ( 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 91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 TYR cc_start: 0.5361 (m-80) cc_final: 0.4760 (m-10) REVERT: A 557 MET cc_start: 0.7564 (ttm) cc_final: 0.7294 (mtp) REVERT: A 623 ARG cc_start: 0.6996 (ttt90) cc_final: 0.5856 (ttp-170) REVERT: A 640 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.7086 (t80) outliers start: 15 outliers final: 11 residues processed: 87 average time/residue: 0.0521 time to fit residues: 6.2338 Evaluate side-chains 83 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 99 ILE Chi-restraints excluded: chain A residue 106 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 530 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.175639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130951 restraints weight = 4789.656| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.16 r_work: 0.3262 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4489 Z= 0.138 Angle : 0.561 7.267 6096 Z= 0.285 Chirality : 0.040 0.127 705 Planarity : 0.004 0.038 735 Dihedral : 6.975 69.375 706 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.09 % Allowed : 18.97 % 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: 1.18 (0.36), residues: 552 helix: 1.90 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.37 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.020 0.001 TYR A 590 PHE 0.017 0.001 PHE A 175 TRP 0.004 0.001 TRP A 259 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4479) covalent geometry : angle 0.55741 ( 6073) SS BOND : bond 0.00197 ( 7) SS BOND : angle 0.84027 ( 14) hydrogen bonds : bond 0.04074 ( 276) hydrogen bonds : angle 4.58038 ( 813) link_BETA1-4 : bond 0.00341 ( 1) link_BETA1-4 : angle 0.84990 ( 3) link_NAG-ASN : bond 0.00241 ( 2) link_NAG-ASN : angle 1.85041 ( 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 93 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.8358 (tpp) cc_final: 0.8109 (tpp) REVERT: A 517 TYR cc_start: 0.5557 (m-80) cc_final: 0.4940 (m-10) REVERT: A 623 ARG cc_start: 0.7184 (ttt90) cc_final: 0.5964 (ttt180) REVERT: A 640 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7237 (t80) outliers start: 19 outliers final: 17 residues processed: 87 average time/residue: 0.0498 time to fit residues: 6.0276 Evaluate side-chains 90 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 99 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 473 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 50 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.177088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132680 restraints weight = 4743.788| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.12 r_work: 0.3281 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.3399 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= 0.127 Angle : 0.549 7.272 6096 Z= 0.282 Chirality : 0.039 0.137 705 Planarity : 0.004 0.037 735 Dihedral : 6.947 68.491 706 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.66 % Allowed : 19.40 % 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: 1.26 (0.36), residues: 552 helix: 1.93 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.24 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 93 TYR 0.021 0.001 TYR A 338 PHE 0.017 0.001 PHE A 175 TRP 0.005 0.001 TRP A 259 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4479) covalent geometry : angle 0.54559 ( 6073) SS BOND : bond 0.00199 ( 7) SS BOND : angle 0.85687 ( 14) hydrogen bonds : bond 0.03983 ( 276) hydrogen bonds : angle 4.54898 ( 813) link_BETA1-4 : bond 0.00362 ( 1) link_BETA1-4 : angle 0.89180 ( 3) link_NAG-ASN : bond 0.00226 ( 2) link_NAG-ASN : angle 1.75354 ( 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 91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.8332 (tpp) cc_final: 0.8041 (tpp) REVERT: A 517 TYR cc_start: 0.5478 (m-80) cc_final: 0.4868 (m-10) REVERT: A 557 MET cc_start: 0.7656 (ttm) cc_final: 0.7333 (mtp) REVERT: A 623 ARG cc_start: 0.7192 (ttt90) cc_final: 0.5956 (ttt180) REVERT: A 640 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7204 (t80) outliers start: 17 outliers final: 13 residues processed: 85 average time/residue: 0.0461 time to fit residues: 5.4743 Evaluate side-chains 86 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 196 ILE 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 603 SER Chi-restraints excluded: chain A residue 624 VAL 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: 0.6980 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.175660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.131460 restraints weight = 4741.814| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.10 r_work: 0.3268 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 4489 Z= 0.144 Angle : 0.560 7.092 6096 Z= 0.288 Chirality : 0.040 0.148 705 Planarity : 0.004 0.037 735 Dihedral : 6.964 68.026 706 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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: 1.29 (0.36), residues: 552 helix: 1.84 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.08 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 93 TYR 0.020 0.001 TYR A 590 PHE 0.018 0.001 PHE A 175 TRP 0.004 0.001 TRP A 259 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4479) covalent geometry : angle 0.55627 ( 6073) SS BOND : bond 0.00210 ( 7) SS BOND : angle 0.91071 ( 14) hydrogen bonds : bond 0.04073 ( 276) hydrogen bonds : angle 4.57464 ( 813) link_BETA1-4 : bond 0.00351 ( 1) link_BETA1-4 : angle 0.94501 ( 3) link_NAG-ASN : bond 0.00191 ( 2) link_NAG-ASN : angle 1.69300 ( 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 87 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.8352 (tpp) cc_final: 0.8104 (tpp) REVERT: A 517 TYR cc_start: 0.5556 (m-80) cc_final: 0.4948 (m-10) REVERT: A 557 MET cc_start: 0.7696 (ttm) cc_final: 0.7402 (mtp) REVERT: A 623 ARG cc_start: 0.7180 (ttt90) cc_final: 0.5944 (ttt180) REVERT: A 640 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7196 (t80) outliers start: 15 outliers final: 13 residues processed: 82 average time/residue: 0.0530 time to fit residues: 5.9588 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 : 0.147 ------------------------------------------------------------------------------- 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 86 TYR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 196 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.178425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133634 restraints weight = 4852.737| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.19 r_work: 0.3321 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4489 Z= 0.120 Angle : 0.539 7.256 6096 Z= 0.279 Chirality : 0.039 0.149 705 Planarity : 0.004 0.036 735 Dihedral : 6.921 67.155 706 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.02 % Allowed : 20.47 % 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: 1.44 (0.36), residues: 552 helix: 2.03 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.09 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 253 TYR 0.020 0.001 TYR A 338 PHE 0.016 0.001 PHE A 175 TRP 0.005 0.001 TRP A 259 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4479) covalent geometry : angle 0.53581 ( 6073) SS BOND : bond 0.00200 ( 7) SS BOND : angle 0.82202 ( 14) hydrogen bonds : bond 0.03871 ( 276) hydrogen bonds : angle 4.49996 ( 813) link_BETA1-4 : bond 0.00317 ( 1) link_BETA1-4 : angle 0.95037 ( 3) link_NAG-ASN : bond 0.00203 ( 2) link_NAG-ASN : angle 1.60517 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1065.47 seconds wall clock time: 18 minutes 56.29 seconds (1136.29 seconds total)