Starting phenix.real_space_refine on Fri Aug 22 19:22:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t1j_40969/08_2025/8t1j_40969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t1j_40969/08_2025/8t1j_40969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t1j_40969/08_2025/8t1j_40969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t1j_40969/08_2025/8t1j_40969.map" model { file = "/net/cci-nas-00/data/ceres_data/8t1j_40969/08_2025/8t1j_40969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t1j_40969/08_2025/8t1j_40969.cif" } resolution = 2.7 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= 0.001 sd= 0.121 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 Zn 1 6.06 5 S 42 5.16 5 C 4460 2.51 5 N 1202 2.21 5 O 1266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6973 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3414 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 396} Chain: "B" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3414 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 396} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {' ZN': 1, 'H4B': 1, 'HEM': 1} Inner-chain residues flagged as termini: ['pdbres="ARG A1502 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'H4B': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 234 SG CYS A 326 33.487 54.832 48.590 1.00 0.00 S ATOM 274 SG CYS A 331 33.594 52.036 51.805 1.00 0.00 S ATOM 3648 SG CYS B 326 36.099 54.944 52.568 1.00 0.00 S ATOM 3688 SG CYS B 331 36.316 52.165 49.106 1.00 0.00 S ATOM 965 SG CYS A 415 42.977 42.732 34.962 1.00 0.00 S ATOM 4379 SG CYS B 415 28.567 40.706 65.373 1.00 0.00 S Time building chain proxies: 1.62, per 1000 atoms: 0.23 Number of scatterers: 6973 At special positions: 0 Unit cell: (74.13, 83.661, 101.664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Fe 2 26.01 S 42 16.00 O 1266 8.00 N 1202 7.00 C 4460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 258.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 331 " pdb="ZN ZN A1501 " - pdb=" SG CYS B 331 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 326 " pdb="ZN ZN A1501 " - pdb=" SG CYS B 326 " Number of angles added : 6 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 16 sheets defined 44.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 350 through 369 Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 397 through 411 Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 434 through 451 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 498 through 507 Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 590 through 595 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 620 through 623 Processing helix chain 'A' and resid 624 through 644 Processing helix chain 'A' and resid 650 through 669 Processing helix chain 'A' and resid 675 through 680 Processing helix chain 'A' and resid 684 through 693 Proline residue: A 689 - end of helix removed outlier: 3.627A pdb=" N HIS A 692 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 713 Processing helix chain 'B' and resid 315 through 320 Processing helix chain 'B' and resid 350 through 369 Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 397 through 411 Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 434 through 451 Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 498 through 507 Processing helix chain 'B' and resid 537 through 541 Processing helix chain 'B' and resid 553 through 558 Processing helix chain 'B' and resid 590 through 595 Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 620 through 623 Processing helix chain 'B' and resid 624 through 644 Processing helix chain 'B' and resid 650 through 669 Processing helix chain 'B' and resid 675 through 680 Processing helix chain 'B' and resid 684 through 693 removed outlier: 3.508A pdb=" N ILE B 687 " --> pdb=" O SER B 684 " (cutoff:3.500A) Proline residue: B 689 - end of helix Processing helix chain 'B' and resid 709 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 301 through 304 Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 331 Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 428 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'A' and resid 484 through 486 Processing sheet with id=AA6, first strand: chain 'A' and resid 543 through 545 Processing sheet with id=AA7, first strand: chain 'A' and resid 577 through 579 Processing sheet with id=AA8, first strand: chain 'A' and resid 588 through 589 removed outlier: 6.470A pdb=" N TYR A 588 " --> pdb=" O VAL A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 697 through 698 Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 304 Processing sheet with id=AB2, first strand: chain 'B' and resid 425 through 428 Processing sheet with id=AB3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'B' and resid 484 through 486 Processing sheet with id=AB5, first strand: chain 'B' and resid 543 through 545 Processing sheet with id=AB6, first strand: chain 'B' and resid 577 through 579 Processing sheet with id=AB7, first strand: chain 'B' and resid 588 through 589 removed outlier: 6.526A pdb=" N TYR B 588 " --> pdb=" O VAL B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 296 hydrogen bonds defined for protein. 732 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: 0.95 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 2923 1.40 - 1.59: 4185 1.59 - 1.78: 2 1.78 - 1.98: 65 1.98 - 2.17: 5 Bond restraints: 7180 Sorted by residual: bond pdb=" C3B HEM B1503 " pdb=" CAB HEM B1503 " ideal model delta sigma weight residual 1.544 1.391 0.153 2.00e-02 2.50e+03 5.81e+01 bond pdb=" C3B HEM A1504 " pdb=" CAB HEM A1504 " ideal model delta sigma weight residual 1.544 1.394 0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" C3C HEM B1503 " pdb=" CAC HEM B1503 " ideal model delta sigma weight residual 1.544 1.402 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C3C HEM A1504 " pdb=" CAC HEM A1504 " ideal model delta sigma weight residual 1.544 1.409 0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" C4A H4B A1503 " pdb=" N5 H4B A1503 " ideal model delta sigma weight residual 1.368 1.465 -0.097 1.60e-02 3.91e+03 3.68e+01 ... (remaining 7175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.38: 9692 5.38 - 10.76: 74 10.76 - 16.15: 2 16.15 - 21.53: 0 21.53 - 26.91: 2 Bond angle restraints: 9770 Sorted by residual: angle pdb=" N LEU A 354 " pdb=" CA LEU A 354 " pdb=" C LEU A 354 " ideal model delta sigma weight residual 111.36 119.13 -7.77 1.09e+00 8.42e-01 5.08e+01 angle pdb=" N LEU B 354 " pdb=" CA LEU B 354 " pdb=" C LEU B 354 " ideal model delta sigma weight residual 111.36 119.12 -7.76 1.09e+00 8.42e-01 5.07e+01 angle pdb=" N VAL B 499 " pdb=" CA VAL B 499 " pdb=" C VAL B 499 " ideal model delta sigma weight residual 110.42 116.18 -5.76 9.60e-01 1.09e+00 3.59e+01 angle pdb=" N1 H4B B1502 " pdb=" C2 H4B B1502 " pdb=" N3 H4B B1502 " ideal model delta sigma weight residual 123.14 117.15 5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" N ASN A 712 " pdb=" CA ASN A 712 " pdb=" C ASN A 712 " ideal model delta sigma weight residual 113.17 105.66 7.51 1.26e+00 6.30e-01 3.55e+01 ... (remaining 9765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 4088 21.64 - 43.28: 95 43.28 - 64.92: 29 64.92 - 86.56: 10 86.56 - 108.20: 8 Dihedral angle restraints: 4230 sinusoidal: 1778 harmonic: 2452 Sorted by residual: dihedral pdb=" C2B HEM A1504 " pdb=" C3B HEM A1504 " pdb=" CAB HEM A1504 " pdb=" CBB HEM A1504 " ideal model delta sinusoidal sigma weight residual 180.00 -101.42 -78.58 2 1.00e+01 1.00e-02 4.61e+01 dihedral pdb=" C2B HEM B1503 " pdb=" C3B HEM B1503 " pdb=" CAB HEM B1503 " pdb=" CBB HEM B1503 " ideal model delta sinusoidal sigma weight residual -180.00 -118.80 -61.20 2 1.00e+01 1.00e-02 3.69e+01 dihedral pdb=" CA TYR A 588 " pdb=" C TYR A 588 " pdb=" N MET A 589 " pdb=" CA MET A 589 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 4227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 676 0.070 - 0.139: 265 0.139 - 0.209: 56 0.209 - 0.278: 15 0.278 - 0.348: 2 Chirality restraints: 1014 Sorted by residual: chirality pdb=" CA VAL B 474 " pdb=" N VAL B 474 " pdb=" C VAL B 474 " pdb=" CB VAL B 474 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA ASP B 471 " pdb=" N ASP B 471 " pdb=" C ASP B 471 " pdb=" CB ASP B 471 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ASP B 347 " pdb=" N ASP B 347 " pdb=" C ASP B 347 " pdb=" CB ASP B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1011 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEM A1504 " 0.015 2.00e-02 2.50e+03 1.26e-01 3.55e+02 pdb=" C2A HEM A1504 " 0.038 2.00e-02 2.50e+03 pdb=" C3A HEM A1504 " 0.104 2.00e-02 2.50e+03 pdb=" C4A HEM A1504 " 0.015 2.00e-02 2.50e+03 pdb=" CAA HEM A1504 " -0.251 2.00e-02 2.50e+03 pdb=" CHA HEM A1504 " 0.100 2.00e-02 2.50e+03 pdb=" CHB HEM A1504 " -0.174 2.00e-02 2.50e+03 pdb=" CMA HEM A1504 " 0.162 2.00e-02 2.50e+03 pdb=" NA HEM A1504 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND HEM B1503 " -0.136 2.00e-02 2.50e+03 1.08e-01 2.62e+02 pdb=" C1D HEM B1503 " -0.147 2.00e-02 2.50e+03 pdb=" C2D HEM B1503 " -0.080 2.00e-02 2.50e+03 pdb=" C3D HEM B1503 " -0.024 2.00e-02 2.50e+03 pdb=" C4D HEM B1503 " -0.002 2.00e-02 2.50e+03 pdb=" CAD HEM B1503 " -0.003 2.00e-02 2.50e+03 pdb=" CHA HEM B1503 " 0.145 2.00e-02 2.50e+03 pdb=" CHD HEM B1503 " 0.179 2.00e-02 2.50e+03 pdb=" CMD HEM B1503 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM A1504 " 0.164 2.00e-02 2.50e+03 1.01e-01 2.28e+02 pdb=" C1B HEM A1504 " 0.019 2.00e-02 2.50e+03 pdb=" C2B HEM A1504 " -0.013 2.00e-02 2.50e+03 pdb=" C3B HEM A1504 " -0.003 2.00e-02 2.50e+03 pdb=" C4B HEM A1504 " 0.071 2.00e-02 2.50e+03 pdb=" CAB HEM A1504 " -0.092 2.00e-02 2.50e+03 pdb=" CHB HEM A1504 " -0.181 2.00e-02 2.50e+03 pdb=" CHC HEM A1504 " -0.074 2.00e-02 2.50e+03 pdb=" CMB HEM A1504 " 0.108 2.00e-02 2.50e+03 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 3409 2.98 - 3.46: 6712 3.46 - 3.94: 12102 3.94 - 4.42: 14631 4.42 - 4.90: 22157 Nonbonded interactions: 59011 Sorted by model distance: nonbonded pdb=" N ASN B 712 " pdb=" N THR B 713 " model vdw 2.502 2.560 nonbonded pdb=" N ASN A 712 " pdb=" N THR A 713 " model vdw 2.502 2.560 nonbonded pdb=" O THR B 433 " pdb=" ND2 ASN B 527 " model vdw 2.525 3.120 nonbonded pdb=" OE1 GLN B 478 " pdb=" NH1 ARG B 481 " model vdw 2.526 3.120 nonbonded pdb=" O THR A 433 " pdb=" ND2 ASN A 527 " model vdw 2.531 3.120 ... (remaining 59006 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 298 through 716 or resid 1502 through 1504)) selection = chain 'B' } 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: 1.970 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.970 Find NCS groups from input model: 0.070 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.015 0.461 7186 Z= 0.717 Angle : 1.479 26.910 9776 Z= 0.970 Chirality : 0.075 0.348 1014 Planarity : 0.011 0.126 1240 Dihedral : 12.837 108.198 2646 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.15 (0.26), residues: 834 helix: -0.01 (0.26), residues: 296 sheet: 0.14 (0.56), residues: 78 loop : 0.33 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 414 TYR 0.100 0.016 TYR A 604 PHE 0.035 0.003 PHE B 554 TRP 0.065 0.006 TRP B 711 HIS 0.009 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.01174 ( 7180) covalent geometry : angle 1.44695 ( 9770) hydrogen bonds : bond 0.21465 ( 296) hydrogen bonds : angle 7.16934 ( 732) metal coordination : bond 0.26405 ( 4) metal coordination : angle 12.43868 ( 6) Misc. bond : bond 0.45764 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.186 Fit side-chains REVERT: B 369 ILE cc_start: 0.7254 (pt) cc_final: 0.7049 (pt) REVERT: B 695 MET cc_start: 0.8951 (mtt) cc_final: 0.8687 (mtt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.6594 time to fit residues: 98.5815 Evaluate side-chains 84 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 GLN A 535 GLN B 385 ASN ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.126557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099465 restraints weight = 8542.914| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.00 r_work: 0.3125 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7186 Z= 0.141 Angle : 0.643 16.949 9776 Z= 0.304 Chirality : 0.043 0.137 1014 Planarity : 0.004 0.034 1240 Dihedral : 11.412 99.478 962 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.39 % Allowed : 8.24 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.39 (0.29), residues: 834 helix: 1.45 (0.30), residues: 310 sheet: 0.12 (0.62), residues: 76 loop : 0.88 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 414 TYR 0.011 0.001 TYR B 666 PHE 0.014 0.002 PHE B 300 TRP 0.008 0.001 TRP B 711 HIS 0.016 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7180) covalent geometry : angle 0.63693 ( 9770) hydrogen bonds : bond 0.04723 ( 296) hydrogen bonds : angle 4.69044 ( 732) metal coordination : bond 0.00879 ( 4) metal coordination : angle 3.55444 ( 6) Misc. bond : bond 0.00797 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.294 Fit side-chains REVERT: A 355 PHE cc_start: 0.7465 (m-80) cc_final: 0.7206 (m-80) REVERT: A 452 LYS cc_start: 0.8772 (mttt) cc_final: 0.8261 (mtmp) REVERT: A 550 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7274 (tppt) REVERT: A 601 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8172 (m-40) REVERT: A 605 ASN cc_start: 0.8299 (t0) cc_final: 0.8086 (t160) REVERT: B 351 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7130 (mttp) REVERT: B 527 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8222 (t0) REVERT: B 573 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: B 614 MET cc_start: 0.8366 (mtp) cc_final: 0.8145 (mtp) REVERT: B 620 LYS cc_start: 0.7887 (mmtt) cc_final: 0.7204 (ptmm) REVERT: B 695 MET cc_start: 0.9046 (mtt) cc_final: 0.8814 (mtt) outliers start: 18 outliers final: 7 residues processed: 100 average time/residue: 0.7280 time to fit residues: 75.7542 Evaluate side-chains 90 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain B residue 668 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN A 712 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.097499 restraints weight = 8597.120| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.01 r_work: 0.3102 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7186 Z= 0.142 Angle : 0.621 17.414 9776 Z= 0.284 Chirality : 0.043 0.136 1014 Planarity : 0.004 0.038 1240 Dihedral : 11.067 98.334 962 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.79 % Allowed : 9.97 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.35 (0.29), residues: 834 helix: 1.49 (0.30), residues: 310 sheet: 0.43 (0.57), residues: 96 loop : 0.73 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 414 TYR 0.010 0.001 TYR A 366 PHE 0.017 0.002 PHE B 355 TRP 0.008 0.001 TRP B 711 HIS 0.012 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7180) covalent geometry : angle 0.61561 ( 9770) hydrogen bonds : bond 0.04555 ( 296) hydrogen bonds : angle 4.54099 ( 732) metal coordination : bond 0.00607 ( 4) metal coordination : angle 3.47739 ( 6) Misc. bond : bond 0.01809 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.352 Fit side-chains REVERT: A 452 LYS cc_start: 0.8787 (mttt) cc_final: 0.8438 (mtmt) REVERT: A 601 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8286 (m110) REVERT: B 351 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6739 (mttp) REVERT: B 491 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.7995 (m) REVERT: B 527 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8230 (t0) REVERT: B 573 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: B 614 MET cc_start: 0.8356 (mtp) cc_final: 0.8125 (mtp) REVERT: B 620 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7210 (ptmm) outliers start: 21 outliers final: 11 residues processed: 97 average time/residue: 0.7071 time to fit residues: 71.3410 Evaluate side-chains 93 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 668 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.0010 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN A 692 HIS A 712 ASN B 535 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.122910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095555 restraints weight = 8636.372| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.00 r_work: 0.3060 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7186 Z= 0.190 Angle : 0.656 17.076 9776 Z= 0.300 Chirality : 0.044 0.146 1014 Planarity : 0.004 0.040 1240 Dihedral : 11.414 102.828 962 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.59 % Allowed : 9.97 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.01 (0.29), residues: 834 helix: 1.09 (0.29), residues: 318 sheet: 0.33 (0.56), residues: 96 loop : 0.60 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 481 TYR 0.011 0.002 TYR A 366 PHE 0.037 0.002 PHE B 355 TRP 0.009 0.002 TRP A 678 HIS 0.010 0.002 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 7180) covalent geometry : angle 0.65035 ( 9770) hydrogen bonds : bond 0.04944 ( 296) hydrogen bonds : angle 4.68077 ( 732) metal coordination : bond 0.00640 ( 4) metal coordination : angle 3.63809 ( 6) Misc. bond : bond 0.01659 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.295 Fit side-chains REVERT: A 371 ARG cc_start: 0.7753 (mmt-90) cc_final: 0.7218 (tpp80) REVERT: A 391 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7482 (p) REVERT: B 351 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6980 (mttp) REVERT: B 491 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.7934 (m) REVERT: B 527 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8309 (t0) REVERT: B 573 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7170 (tm-30) REVERT: B 614 MET cc_start: 0.8457 (mtp) cc_final: 0.8179 (mtp) REVERT: B 620 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7216 (ptmm) outliers start: 27 outliers final: 15 residues processed: 97 average time/residue: 0.6802 time to fit residues: 68.8454 Evaluate side-chains 99 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 686 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS A 605 ASN A 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.124752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.097651 restraints weight = 8638.184| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.99 r_work: 0.3112 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7186 Z= 0.127 Angle : 0.562 14.049 9776 Z= 0.265 Chirality : 0.042 0.134 1014 Planarity : 0.004 0.042 1240 Dihedral : 10.807 97.000 962 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.66 % Allowed : 11.17 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.19 (0.30), residues: 834 helix: 1.33 (0.30), residues: 314 sheet: 0.28 (0.56), residues: 96 loop : 0.67 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.010 0.001 TYR B 366 PHE 0.036 0.002 PHE B 355 TRP 0.010 0.001 TRP B 587 HIS 0.010 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7180) covalent geometry : angle 0.55651 ( 9770) hydrogen bonds : bond 0.04128 ( 296) hydrogen bonds : angle 4.48159 ( 732) metal coordination : bond 0.00371 ( 4) metal coordination : angle 3.31141 ( 6) Misc. bond : bond 0.01285 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.205 Fit side-chains REVERT: A 371 ARG cc_start: 0.7724 (mmt-90) cc_final: 0.7125 (tpp80) REVERT: A 391 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7479 (p) REVERT: A 573 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: B 491 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.7969 (m) REVERT: B 573 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: B 614 MET cc_start: 0.8398 (mtp) cc_final: 0.8138 (mtp) REVERT: B 620 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7215 (ptmm) outliers start: 20 outliers final: 10 residues processed: 94 average time/residue: 0.6958 time to fit residues: 68.3243 Evaluate side-chains 88 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 668 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN A 712 ASN B 317 HIS B 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.094907 restraints weight = 8664.758| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.99 r_work: 0.3060 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 7186 Z= 0.230 Angle : 0.670 16.243 9776 Z= 0.309 Chirality : 0.046 0.142 1014 Planarity : 0.004 0.041 1240 Dihedral : 11.594 104.394 962 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.06 % Allowed : 11.17 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.85 (0.29), residues: 834 helix: 1.02 (0.29), residues: 318 sheet: 0.20 (0.56), residues: 96 loop : 0.46 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 481 TYR 0.011 0.002 TYR A 366 PHE 0.037 0.002 PHE B 355 TRP 0.011 0.002 TRP A 678 HIS 0.008 0.002 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 7180) covalent geometry : angle 0.66333 ( 9770) hydrogen bonds : bond 0.05225 ( 296) hydrogen bonds : angle 4.73126 ( 732) metal coordination : bond 0.00499 ( 4) metal coordination : angle 3.79672 ( 6) Misc. bond : bond 0.01013 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.286 Fit side-chains REVERT: A 300 PHE cc_start: 0.7194 (m-80) cc_final: 0.6768 (p90) REVERT: A 349 ARG cc_start: 0.6549 (tpp80) cc_final: 0.6241 (mtt90) REVERT: A 371 ARG cc_start: 0.7749 (mmt-90) cc_final: 0.7311 (tpp80) REVERT: A 391 THR cc_start: 0.7887 (OUTLIER) cc_final: 0.7671 (p) REVERT: A 573 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: B 299 ARG cc_start: 0.5749 (mmp80) cc_final: 0.5072 (tpp-160) REVERT: B 328 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6906 (tp30) REVERT: B 491 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.7934 (m) REVERT: B 573 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: B 614 MET cc_start: 0.8567 (mtp) cc_final: 0.8335 (mtp) outliers start: 23 outliers final: 14 residues processed: 93 average time/residue: 0.6476 time to fit residues: 62.9602 Evaluate side-chains 96 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 686 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 62 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 19 optimal weight: 0.0000 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 712 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.124199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097153 restraints weight = 8585.907| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.98 r_work: 0.3105 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7186 Z= 0.131 Angle : 0.571 13.234 9776 Z= 0.273 Chirality : 0.042 0.136 1014 Planarity : 0.004 0.043 1240 Dihedral : 10.934 97.697 962 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.53 % Allowed : 11.84 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.04 (0.29), residues: 834 helix: 1.28 (0.30), residues: 314 sheet: 0.24 (0.55), residues: 96 loop : 0.50 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.009 0.001 TYR B 366 PHE 0.039 0.002 PHE B 355 TRP 0.010 0.001 TRP B 587 HIS 0.009 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7180) covalent geometry : angle 0.56419 ( 9770) hydrogen bonds : bond 0.04168 ( 296) hydrogen bonds : angle 4.50590 ( 732) metal coordination : bond 0.00344 ( 4) metal coordination : angle 3.49816 ( 6) Misc. bond : bond 0.01115 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.278 Fit side-chains REVERT: A 300 PHE cc_start: 0.7121 (m-80) cc_final: 0.6768 (p90) REVERT: A 349 ARG cc_start: 0.6435 (tpp80) cc_final: 0.6232 (mtt90) REVERT: A 355 PHE cc_start: 0.7764 (m-80) cc_final: 0.7520 (m-80) REVERT: A 371 ARG cc_start: 0.7710 (mmt-90) cc_final: 0.7208 (tpp80) REVERT: A 391 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7552 (p) REVERT: A 573 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: B 299 ARG cc_start: 0.5794 (mmp80) cc_final: 0.5112 (tpp-160) REVERT: B 328 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6841 (tp30) REVERT: B 438 MET cc_start: 0.8770 (mtp) cc_final: 0.8420 (mtp) REVERT: B 491 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.7975 (m) REVERT: B 573 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: B 614 MET cc_start: 0.8532 (mtp) cc_final: 0.8266 (mtp) outliers start: 19 outliers final: 10 residues processed: 92 average time/residue: 0.6436 time to fit residues: 61.8294 Evaluate side-chains 92 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 686 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.0670 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 605 ASN A 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.096601 restraints weight = 8676.537| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.00 r_work: 0.3087 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7186 Z= 0.151 Angle : 0.587 13.903 9776 Z= 0.278 Chirality : 0.043 0.138 1014 Planarity : 0.004 0.042 1240 Dihedral : 11.011 100.018 962 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.13 % Allowed : 11.84 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 0.97 (0.29), residues: 834 helix: 1.20 (0.29), residues: 318 sheet: 0.26 (0.55), residues: 96 loop : 0.45 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 465 TYR 0.010 0.001 TYR B 366 PHE 0.041 0.002 PHE B 355 TRP 0.009 0.001 TRP B 587 HIS 0.009 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 7180) covalent geometry : angle 0.58051 ( 9770) hydrogen bonds : bond 0.04382 ( 296) hydrogen bonds : angle 4.52901 ( 732) metal coordination : bond 0.00419 ( 4) metal coordination : angle 3.53311 ( 6) Misc. bond : bond 0.01065 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.233 Fit side-chains REVERT: A 300 PHE cc_start: 0.7163 (m-80) cc_final: 0.6798 (p90) REVERT: A 349 ARG cc_start: 0.6598 (tpp80) cc_final: 0.6391 (mtt90) REVERT: A 355 PHE cc_start: 0.7897 (m-80) cc_final: 0.7599 (m-80) REVERT: A 371 ARG cc_start: 0.7757 (mmt-90) cc_final: 0.7221 (tpp80) REVERT: A 573 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: B 299 ARG cc_start: 0.5724 (mmp80) cc_final: 0.5080 (tpp-160) REVERT: B 328 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6915 (tp30) REVERT: B 438 MET cc_start: 0.8782 (mtp) cc_final: 0.8447 (mtp) REVERT: B 491 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.7968 (m) REVERT: B 573 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: B 614 MET cc_start: 0.8543 (mtp) cc_final: 0.8280 (mtp) outliers start: 16 outliers final: 11 residues processed: 90 average time/residue: 0.6653 time to fit residues: 62.4818 Evaluate side-chains 89 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 686 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 44 optimal weight: 0.0870 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 605 ASN A 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.097490 restraints weight = 8597.501| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.97 r_work: 0.3104 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7186 Z= 0.130 Angle : 0.568 12.806 9776 Z= 0.272 Chirality : 0.042 0.139 1014 Planarity : 0.004 0.043 1240 Dihedral : 10.774 97.844 962 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.13 % Allowed : 11.84 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.09 (0.29), residues: 834 helix: 1.35 (0.30), residues: 314 sheet: 0.29 (0.55), residues: 96 loop : 0.49 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 465 TYR 0.010 0.001 TYR B 366 PHE 0.045 0.002 PHE B 355 TRP 0.011 0.001 TRP B 587 HIS 0.009 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 7180) covalent geometry : angle 0.56195 ( 9770) hydrogen bonds : bond 0.04096 ( 296) hydrogen bonds : angle 4.47227 ( 732) metal coordination : bond 0.00382 ( 4) metal coordination : angle 3.45489 ( 6) Misc. bond : bond 0.01086 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.303 Fit side-chains REVERT: A 300 PHE cc_start: 0.7130 (m-80) cc_final: 0.6794 (p90) REVERT: A 371 ARG cc_start: 0.7722 (mmt-90) cc_final: 0.7151 (tpp80) REVERT: A 573 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: B 299 ARG cc_start: 0.5681 (mmp80) cc_final: 0.5103 (tpp-160) REVERT: B 328 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6869 (tp30) REVERT: B 491 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.8007 (m) REVERT: B 573 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: B 614 MET cc_start: 0.8463 (mtp) cc_final: 0.8183 (mtp) outliers start: 16 outliers final: 11 residues processed: 89 average time/residue: 0.6731 time to fit residues: 62.4646 Evaluate side-chains 90 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 686 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 46 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.0570 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN A 712 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.097067 restraints weight = 8562.397| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.98 r_work: 0.3088 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7186 Z= 0.143 Angle : 0.579 13.333 9776 Z= 0.275 Chirality : 0.042 0.141 1014 Planarity : 0.004 0.043 1240 Dihedral : 10.845 98.779 962 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.99 % Allowed : 12.37 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.08 (0.29), residues: 834 helix: 1.33 (0.30), residues: 314 sheet: 0.32 (0.55), residues: 96 loop : 0.48 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 349 TYR 0.010 0.001 TYR B 366 PHE 0.046 0.002 PHE B 355 TRP 0.010 0.001 TRP B 587 HIS 0.009 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7180) covalent geometry : angle 0.57331 ( 9770) hydrogen bonds : bond 0.04234 ( 296) hydrogen bonds : angle 4.49532 ( 732) metal coordination : bond 0.00415 ( 4) metal coordination : angle 3.43284 ( 6) Misc. bond : bond 0.01017 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.192 Fit side-chains REVERT: A 300 PHE cc_start: 0.7134 (m-80) cc_final: 0.6808 (p90) REVERT: A 371 ARG cc_start: 0.7713 (mmt-90) cc_final: 0.7188 (tpp80) REVERT: A 573 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: B 299 ARG cc_start: 0.5707 (mmp80) cc_final: 0.5112 (tpp-160) REVERT: B 328 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6900 (tp30) REVERT: B 491 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.8019 (m) REVERT: B 573 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: B 614 MET cc_start: 0.8457 (mtp) cc_final: 0.8179 (mtp) outliers start: 15 outliers final: 11 residues processed: 87 average time/residue: 0.6810 time to fit residues: 61.6910 Evaluate side-chains 89 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 573 GLU Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 686 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 56 optimal weight: 0.0070 chunk 61 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN A 712 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.124831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.097990 restraints weight = 8539.327| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.97 r_work: 0.3134 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7186 Z= 0.122 Angle : 0.559 12.141 9776 Z= 0.268 Chirality : 0.042 0.146 1014 Planarity : 0.004 0.043 1240 Dihedral : 10.565 95.646 962 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.99 % Allowed : 12.37 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: 1.16 (0.29), residues: 834 helix: 1.40 (0.30), residues: 314 sheet: 0.35 (0.55), residues: 96 loop : 0.54 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 349 TYR 0.010 0.001 TYR B 366 PHE 0.046 0.002 PHE B 355 TRP 0.011 0.001 TRP B 587 HIS 0.009 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7180) covalent geometry : angle 0.55223 ( 9770) hydrogen bonds : bond 0.03933 ( 296) hydrogen bonds : angle 4.40344 ( 732) metal coordination : bond 0.00367 ( 4) metal coordination : angle 3.47204 ( 6) Misc. bond : bond 0.01064 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2488.30 seconds wall clock time: 43 minutes 1.65 seconds (2581.65 seconds total)