Starting phenix.real_space_refine on Thu Sep 10 23:41:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7slp_25197/09_2026/7slp_25197.cif Found real_map, /net/cci-nas-00/data/ceres_data/7slp_25197/09_2026/7slp_25197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7slp_25197/09_2026/7slp_25197.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7slp_25197/09_2026/7slp_25197.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7slp_25197/09_2026/7slp_25197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7slp_25197/09_2026/7slp_25197.map" model { file = "/net/cci-nas-00/data/ceres_data/7slp_25197/09_2026/7slp_25197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7slp_25197/09_2026/7slp_25197.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 37 5.49 5 S 15 5.16 5 C 3151 2.51 5 N 912 2.21 5 O 1061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5176 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1887 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2481 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 10, 'TRANS': 310} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 782 Classifications: {'RNAv2': 37} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 10, 'rna3p_pyr': 14} Link IDs: {'rna2p': 12, 'rna3p': 24} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 1.42, per 1000 atoms: 0.27 Number of scatterers: 5176 At special positions: 0 Unit cell: (81.32, 78.11, 101.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 37 15.00 O 1061 8.00 N 912 7.00 C 3151 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=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 190.3 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1058 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 4 sheets defined 49.8% alpha, 11.4% beta 8 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 432 through 437 removed outlier: 3.788A pdb=" N VAL A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 437' Processing helix chain 'A' and resid 438 through 442 removed outlier: 4.336A pdb=" N TRP A 441 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 465 Processing helix chain 'A' and resid 476 through 492 removed outlier: 4.035A pdb=" N SER A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.614A pdb=" N THR A 528 " --> pdb=" O PRO A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 583 through 592 Processing helix chain 'A' and resid 593 through 606 Processing helix chain 'A' and resid 630 through 638 removed outlier: 3.872A pdb=" N TYR A 634 " --> pdb=" O THR A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.582A pdb=" N THR A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 55 through 63 Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 77 through 82 removed outlier: 3.537A pdb=" N LYS B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.502A pdb=" N GLU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 413 Processing helix chain 'B' and resid 467 through 479 removed outlier: 3.967A pdb=" N ILE B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 508 Processing helix chain 'B' and resid 509 through 515 removed outlier: 3.810A pdb=" N ILE B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 545 removed outlier: 4.103A pdb=" N GLN B 530 " --> pdb=" O GLY B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 571 Processing sheet with id=AA1, first strand: chain 'A' and resid 554 through 557 removed outlier: 6.611A pdb=" N MET A 470 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL A 556 " --> pdb=" O MET A 470 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY A 472 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 448 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N LEU A 581 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 450 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP A 576 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL A 614 " --> pdb=" O ASP A 576 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A 578 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLU A 616 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N CYS A 580 " --> pdb=" O GLU A 616 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 70 removed outlier: 3.765A pdb=" N VAL B 69 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 101 " --> pdb=" O ARG B 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 153 through 155 removed outlier: 3.749A pdb=" N TYR B 153 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 481 through 485 removed outlier: 6.360A pdb=" N ARG B 496 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL B 484 " --> pdb=" O HIS B 494 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS B 494 " --> pdb=" O VAL B 484 " (cutoff:3.500A) 197 hydrogen bonds defined for protein. 582 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1067 1.33 - 1.45: 1463 1.45 - 1.57: 2736 1.57 - 1.70: 73 1.70 - 1.82: 21 Bond restraints: 5360 Sorted by residual: bond pdb=" N GLU A 574 " pdb=" CA GLU A 574 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.00e-02 1.00e+04 9.22e+00 bond pdb=" C2 SAH A 701 " pdb=" N3 SAH A 701 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" N LYS A 625 " pdb=" CA LYS A 625 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.37e+00 bond pdb=" N SER A 622 " pdb=" CA SER A 622 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.89e+00 bond pdb=" N LYS B 112 " pdb=" CA LYS B 112 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.23e+00 ... (remaining 5355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 6811 2.16 - 4.32: 514 4.32 - 6.48: 82 6.48 - 8.64: 20 8.64 - 10.79: 9 Bond angle restraints: 7436 Sorted by residual: angle pdb=" N LEU B 131 " pdb=" CA LEU B 131 " pdb=" C LEU B 131 " ideal model delta sigma weight residual 110.91 120.44 -9.53 1.17e+00 7.31e-01 6.64e+01 angle pdb=" C PRO A 573 " pdb=" CA PRO A 573 " pdb=" CB PRO A 573 " ideal model delta sigma weight residual 111.11 102.94 8.17 1.17e+00 7.31e-01 4.88e+01 angle pdb=" N GLU B 480 " pdb=" CA GLU B 480 " pdb=" C GLU B 480 " ideal model delta sigma weight residual 109.15 118.31 -9.16 1.44e+00 4.82e-01 4.05e+01 angle pdb=" C SER B 479 " pdb=" CA SER B 479 " pdb=" CB SER B 479 " ideal model delta sigma weight residual 112.78 101.99 10.79 2.18e+00 2.10e-01 2.45e+01 angle pdb=" N LEU B 132 " pdb=" CA LEU B 132 " pdb=" C LEU B 132 " ideal model delta sigma weight residual 110.07 116.14 -6.07 1.26e+00 6.30e-01 2.32e+01 ... (remaining 7431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 2750 21.50 - 42.99: 257 42.99 - 64.48: 101 64.48 - 85.98: 23 85.98 - 107.47: 1 Dihedral angle restraints: 3132 sinusoidal: 1497 harmonic: 1635 Sorted by residual: dihedral pdb=" C4' G R 308 " pdb=" C3' G R 308 " pdb=" C2' G R 308 " pdb=" C1' G R 308 " ideal model delta sinusoidal sigma weight residual 36.35 -40.33 76.68 1 3.10e+00 1.04e-01 7.69e+02 dihedral pdb=" C4' G R 300 " pdb=" C3' G R 300 " pdb=" C2' G R 300 " pdb=" C1' G R 300 " ideal model delta sinusoidal sigma weight residual 36.34 -38.46 74.81 1 3.10e+00 1.04e-01 7.37e+02 dihedral pdb=" C4' A R 301 " pdb=" C3' A R 301 " pdb=" C2' A R 301 " pdb=" C1' A R 301 " ideal model delta sinusoidal sigma weight residual 36.35 -37.62 73.96 1 3.10e+00 1.04e-01 7.23e+02 ... (remaining 3129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 685 0.086 - 0.173: 99 0.173 - 0.259: 60 0.259 - 0.345: 18 0.345 - 0.432: 5 Chirality restraints: 867 Sorted by residual: chirality pdb=" CB VAL B 99 " pdb=" CA VAL B 99 " pdb=" CG1 VAL B 99 " pdb=" CG2 VAL B 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" P G R 322 " pdb=" OP1 G R 322 " pdb=" OP2 G R 322 " pdb=" O5' G R 322 " both_signs ideal model delta sigma weight residual True 2.17 -2.57 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C2' G R 308 " pdb=" C3' G R 308 " pdb=" O2' G R 308 " pdb=" C1' G R 308 " both_signs ideal model delta sigma weight residual False -2.79 -2.43 -0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 864 not shown) Planarity restraints: 807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 643 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO A 644 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 539 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C VAL A 539 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL A 539 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO A 540 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 588 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C HIS A 588 " -0.042 2.00e-02 2.50e+03 pdb=" O HIS A 588 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 589 " 0.014 2.00e-02 2.50e+03 ... (remaining 804 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 814 2.76 - 3.29: 4637 3.29 - 3.83: 9027 3.83 - 4.36: 9825 4.36 - 4.90: 15905 Nonbonded interactions: 40208 Sorted by model distance: nonbonded pdb=" O2' C R 320 " pdb=" OP1 C R 323 " model vdw 2.221 3.040 nonbonded pdb=" O2' U R 327 " pdb=" O2 U R 327 " model vdw 2.233 3.040 nonbonded pdb=" O GLN B 470 " pdb=" OG1 THR B 474 " model vdw 2.298 3.040 nonbonded pdb=" NH2 ARG B 552 " pdb=" N7 G R 303 " model vdw 2.303 3.200 nonbonded pdb=" O ARG A 425 " pdb=" OH TYR A 490 " model vdw 2.306 3.040 ... (remaining 40203 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.080 Find NCS groups from input model: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 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 0.100 5360 Z= 0.410 Angle : 1.302 10.794 7436 Z= 0.688 Chirality : 0.091 0.432 867 Planarity : 0.008 0.065 807 Dihedral : 19.536 107.470 2074 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.20 % Favored : 95.26 % Rotamer: Outliers : 1.77 % Allowed : 9.49 % Favored : 88.74 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.00 % 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: -3.76 (0.27), residues: 548 helix: -3.01 (0.21), residues: 266 sheet: 0.07 (0.64), residues: 60 loop : -2.38 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 484 TYR 0.029 0.005 TYR A 661 PHE 0.033 0.004 PHE A 442 TRP 0.018 0.003 TRP B 384 HIS 0.009 0.003 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00827 / 0.41 ( 5360) covalent geometry : angle 1.30209 / 0.69 ( 7436) hydrogen bonds : bond 0.18290 / 11.87 ( 218) hydrogen bonds : angle 7.77036 / 5.39 ( 616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.7272 (ttt) cc_final: 0.6917 (tmm) REVERT: A 538 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7807 (mt0) REVERT: A 557 THR cc_start: 0.6231 (t) cc_final: 0.5924 (t) REVERT: A 582 SER cc_start: 0.6965 (m) cc_final: 0.6748 (t) REVERT: A 607 LEU cc_start: 0.5854 (mt) cc_final: 0.5625 (mp) REVERT: A 661 TYR cc_start: 0.6298 (p90) cc_final: 0.6024 (p90) REVERT: B 50 ASN cc_start: 0.7391 (t0) cc_final: 0.7144 (t0) REVERT: B 123 ASP cc_start: 0.8371 (t0) cc_final: 0.8168 (t0) REVERT: B 159 TYR cc_start: 0.6892 (m-80) cc_final: 0.6436 (m-80) outliers start: 8 outliers final: 4 residues processed: 158 average time/residue: 0.0789 time to fit residues: 15.7420 Evaluate side-chains 89 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 30.0000 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 ASN B 50 ASN B 530 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.156774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.131131 restraints weight = 12321.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.133881 restraints weight = 8385.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.135809 restraints weight = 6404.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.136919 restraints weight = 5290.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.137803 restraints weight = 4675.467| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5360 Z= 0.192 Angle : 1.061 16.590 7436 Z= 0.453 Chirality : 0.074 0.645 867 Planarity : 0.007 0.080 807 Dihedral : 16.610 161.176 1057 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.58 (0.32), residues: 548 helix: -0.80 (0.29), residues: 265 sheet: -0.12 (0.64), residues: 63 loop : -1.49 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 488 TYR 0.018 0.002 TYR B 159 PHE 0.024 0.002 PHE B 44 TRP 0.035 0.003 TRP A 586 HIS 0.007 0.002 HIS A 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 ( 5360) covalent geometry : angle 1.06132 / 0.45 ( 7436) hydrogen bonds : bond 0.04898 / 3.17 ( 218) hydrogen bonds : angle 5.17524 / 3.60 ( 616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ASP cc_start: 0.6980 (t0) cc_final: 0.6701 (t0) REVERT: A 452 CYS cc_start: 0.8016 (p) cc_final: 0.7216 (p) REVERT: A 582 SER cc_start: 0.7282 (m) cc_final: 0.6925 (t) REVERT: A 608 ARG cc_start: 0.7561 (mtp85) cc_final: 0.6887 (ptp-170) REVERT: B 77 PHE cc_start: 0.7249 (m-10) cc_final: 0.6853 (m-80) REVERT: B 80 MET cc_start: 0.5300 (tpt) cc_final: 0.4685 (tpt) REVERT: B 408 GLN cc_start: 0.6784 (tm-30) cc_final: 0.6571 (mt0) REVERT: B 519 TRP cc_start: 0.5517 (m-10) cc_final: 0.5296 (m-10) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0796 time to fit residues: 11.5355 Evaluate side-chains 79 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 0.0870 chunk 10 optimal weight: 6.9990 chunk 53 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 HIS B 50 ASN B 395 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.155088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.131156 restraints weight = 12623.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.133117 restraints weight = 9468.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134570 restraints weight = 7707.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.135557 restraints weight = 6622.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.136125 restraints weight = 5975.234| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.7307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5360 Z= 0.178 Angle : 0.883 9.385 7436 Z= 0.402 Chirality : 0.059 0.365 867 Planarity : 0.007 0.096 807 Dihedral : 15.831 174.278 1057 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.69 (0.35), residues: 548 helix: 0.10 (0.32), residues: 266 sheet: -0.34 (0.73), residues: 50 loop : -1.04 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 601 TYR 0.020 0.002 TYR B 159 PHE 0.017 0.002 PHE A 523 TRP 0.040 0.003 TRP A 441 HIS 0.009 0.002 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 5360) covalent geometry : angle 0.88337 / 0.40 ( 7436) hydrogen bonds : bond 0.04321 / 2.79 ( 218) hydrogen bonds : angle 5.01526 / 3.45 ( 616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 582 SER cc_start: 0.7283 (m) cc_final: 0.6895 (t) REVERT: A 630 THR cc_start: 0.6232 (p) cc_final: 0.5857 (p) REVERT: B 38 ILE cc_start: 0.7953 (mt) cc_final: 0.7600 (mt) REVERT: B 154 ILE cc_start: 0.8782 (mt) cc_final: 0.8571 (mp) REVERT: B 408 GLN cc_start: 0.7496 (tm-30) cc_final: 0.7205 (mt0) REVERT: B 519 TRP cc_start: 0.5996 (m-10) cc_final: 0.5796 (m-10) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0666 time to fit residues: 9.0260 Evaluate side-chains 69 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 45 optimal weight: 10.0000 chunk 21 optimal weight: 0.0010 chunk 57 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 453 ASN A 456 HIS A 486 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.149401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.125407 restraints weight = 13122.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.127337 restraints weight = 9790.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.128668 restraints weight = 7929.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.129710 restraints weight = 6815.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.130255 restraints weight = 6126.850| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 1.0178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5360 Z= 0.219 Angle : 0.961 10.806 7436 Z= 0.434 Chirality : 0.062 0.368 867 Planarity : 0.007 0.095 807 Dihedral : 16.105 161.920 1057 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.10 (0.34), residues: 548 helix: -0.22 (0.29), residues: 273 sheet: -0.36 (0.69), residues: 55 loop : -1.36 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 552 TYR 0.016 0.002 TYR B 532 PHE 0.017 0.003 PHE A 523 TRP 0.019 0.002 TRP A 586 HIS 0.008 0.002 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.22 ( 5360) covalent geometry : angle 0.96106 / 0.43 ( 7436) hydrogen bonds : bond 0.05164 / 3.39 ( 218) hydrogen bonds : angle 5.54781 / 3.81 ( 616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8604 (tppp) cc_final: 0.8280 (tptt) REVERT: B 401 SER cc_start: 0.8704 (m) cc_final: 0.8498 (p) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0596 time to fit residues: 7.3839 Evaluate side-chains 68 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 31 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 0.1980 chunk 54 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.1980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.146556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.121517 restraints weight = 13198.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.123837 restraints weight = 9410.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.125447 restraints weight = 7357.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.126621 restraints weight = 6202.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.127040 restraints weight = 5495.022| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 1.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5360 Z= 0.229 Angle : 0.916 8.747 7436 Z= 0.419 Chirality : 0.061 0.410 867 Planarity : 0.007 0.085 807 Dihedral : 16.140 168.370 1057 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.22 % Allowed : 2.65 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.03 (0.34), residues: 548 helix: 0.04 (0.31), residues: 271 sheet: -1.13 (0.65), residues: 57 loop : -1.39 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 95 TYR 0.019 0.002 TYR A 604 PHE 0.021 0.002 PHE B 77 TRP 0.011 0.002 TRP B 384 HIS 0.007 0.002 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.23 ( 5360) covalent geometry : angle 0.91648 / 0.42 ( 7436) hydrogen bonds : bond 0.05137 / 3.44 ( 218) hydrogen bonds : angle 5.31512 / 3.66 ( 616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 ASP cc_start: 0.8253 (t0) cc_final: 0.8036 (t0) REVERT: B 40 LYS cc_start: 0.8640 (tppp) cc_final: 0.8212 (tptt) REVERT: B 145 PHE cc_start: 0.7798 (m-10) cc_final: 0.7337 (m-80) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.0705 time to fit residues: 9.1200 Evaluate side-chains 62 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 3 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.152568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.129119 restraints weight = 12919.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.131192 restraints weight = 9424.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.132693 restraints weight = 7527.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.133569 restraints weight = 6394.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.134460 restraints weight = 5735.926| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 1.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5360 Z= 0.126 Angle : 0.775 8.649 7436 Z= 0.350 Chirality : 0.056 0.339 867 Planarity : 0.006 0.096 807 Dihedral : 15.651 160.110 1057 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.22 % Allowed : 1.10 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.35), residues: 548 helix: 0.50 (0.32), residues: 273 sheet: -0.55 (0.70), residues: 53 loop : -1.29 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 552 TYR 0.018 0.001 TYR A 661 PHE 0.022 0.002 PHE B 77 TRP 0.009 0.001 TRP A 591 HIS 0.005 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 5360) covalent geometry : angle 0.77485 / 0.35 ( 7436) hydrogen bonds : bond 0.03789 / 2.56 ( 218) hydrogen bonds : angle 4.61107 / 3.23 ( 616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 593 ASP cc_start: 0.4471 (m-30) cc_final: 0.3202 (t70) REVERT: A 615 LEU cc_start: 0.6019 (mt) cc_final: 0.4705 (mp) REVERT: B 40 LYS cc_start: 0.8615 (tppp) cc_final: 0.8269 (tptt) REVERT: B 80 MET cc_start: 0.6551 (tpp) cc_final: 0.5994 (tpt) REVERT: B 540 ARG cc_start: 0.6941 (pmt-80) cc_final: 0.6453 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.0641 time to fit residues: 8.3729 Evaluate side-chains 64 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.143837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.120056 restraints weight = 13321.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.121724 restraints weight = 10335.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.122747 restraints weight = 8574.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.123799 restraints weight = 7573.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.124284 restraints weight = 6880.762| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 1.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5360 Z= 0.271 Angle : 0.988 8.017 7436 Z= 0.450 Chirality : 0.066 0.526 867 Planarity : 0.007 0.104 807 Dihedral : 16.358 164.412 1057 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.22 % Allowed : 2.65 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.15 (0.35), residues: 548 helix: -0.08 (0.31), residues: 270 sheet: -0.80 (0.76), residues: 54 loop : -1.52 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 95 TYR 0.014 0.002 TYR B 532 PHE 0.017 0.002 PHE B 497 TRP 0.014 0.003 TRP A 620 HIS 0.010 0.003 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.27 ( 5360) covalent geometry : angle 0.98769 / 0.45 ( 7436) hydrogen bonds : bond 0.05779 / 4.00 ( 218) hydrogen bonds : angle 5.45415 / 3.78 ( 616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 593 ASP cc_start: 0.4768 (m-30) cc_final: 0.3787 (t70) outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.0617 time to fit residues: 6.5838 Evaluate side-chains 58 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.150322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.126525 restraints weight = 13175.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129075 restraints weight = 9107.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.130800 restraints weight = 6956.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.131855 restraints weight = 5747.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.132815 restraints weight = 5049.695| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 1.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5360 Z= 0.124 Angle : 0.789 9.905 7436 Z= 0.348 Chirality : 0.056 0.348 867 Planarity : 0.006 0.094 807 Dihedral : 15.689 159.104 1057 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.22 % Allowed : 1.32 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.64 (0.35), residues: 548 helix: 0.38 (0.32), residues: 272 sheet: -0.64 (0.68), residues: 60 loop : -1.32 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.019 0.001 TYR A 661 PHE 0.016 0.002 PHE B 77 TRP 0.010 0.002 TRP B 384 HIS 0.004 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 5360) covalent geometry : angle 0.78857 / 0.35 ( 7436) hydrogen bonds : bond 0.03758 / 2.52 ( 218) hydrogen bonds : angle 4.61399 / 3.23 ( 616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 ASP cc_start: 0.4497 (m-30) cc_final: 0.3309 (t70) REVERT: A 615 LEU cc_start: 0.6377 (mt) cc_final: 0.5056 (mp) REVERT: B 38 ILE cc_start: 0.7671 (mt) cc_final: 0.7190 (mm) REVERT: B 540 ARG cc_start: 0.7333 (pmt-80) cc_final: 0.6476 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.0504 time to fit residues: 5.7970 Evaluate side-chains 64 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 6 optimal weight: 0.0670 chunk 22 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.150684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.127755 restraints weight = 13128.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.129651 restraints weight = 9866.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.131056 restraints weight = 7977.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.131851 restraints weight = 6849.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.132524 restraints weight = 6183.590| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 1.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5360 Z= 0.122 Angle : 0.773 8.593 7436 Z= 0.343 Chirality : 0.055 0.353 867 Planarity : 0.006 0.107 807 Dihedral : 15.442 158.859 1057 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.22 % Allowed : 0.44 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.32 (0.36), residues: 548 helix: 0.67 (0.33), residues: 272 sheet: -0.35 (0.73), residues: 55 loop : -1.24 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 552 TYR 0.014 0.001 TYR B 391 PHE 0.012 0.001 PHE A 658 TRP 0.010 0.001 TRP A 591 HIS 0.003 0.001 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 5360) covalent geometry : angle 0.77269 / 0.34 ( 7436) hydrogen bonds : bond 0.03734 / 2.54 ( 218) hydrogen bonds : angle 4.53463 / 3.17 ( 616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 593 ASP cc_start: 0.4829 (m-30) cc_final: 0.3707 (t70) REVERT: A 615 LEU cc_start: 0.6056 (mt) cc_final: 0.5529 (mt) REVERT: B 38 ILE cc_start: 0.7652 (mt) cc_final: 0.7191 (mm) REVERT: B 50 ASN cc_start: 0.8284 (t0) cc_final: 0.7958 (t0) REVERT: B 540 ARG cc_start: 0.7129 (pmt-80) cc_final: 0.6372 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.0480 time to fit residues: 5.7182 Evaluate side-chains 64 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 25 optimal weight: 0.1980 chunk 47 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.152460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129646 restraints weight = 13296.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.131589 restraints weight = 9924.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.133051 restraints weight = 8016.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.134013 restraints weight = 6825.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.134653 restraints weight = 6080.664| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 1.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5360 Z= 0.112 Angle : 0.743 8.576 7436 Z= 0.330 Chirality : 0.054 0.358 867 Planarity : 0.006 0.106 807 Dihedral : 15.230 159.176 1057 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.01 (0.36), residues: 548 helix: 0.84 (0.33), residues: 272 sheet: 0.03 (0.74), residues: 54 loop : -1.03 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 552 TYR 0.015 0.001 TYR B 532 PHE 0.013 0.001 PHE B 77 TRP 0.017 0.002 TRP B 533 HIS 0.002 0.001 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 5360) covalent geometry : angle 0.74300 / 0.33 ( 7436) hydrogen bonds : bond 0.03438 / 2.31 ( 218) hydrogen bonds : angle 4.39105 / 3.07 ( 616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 551 ASN cc_start: 0.8341 (p0) cc_final: 0.8095 (p0) REVERT: A 593 ASP cc_start: 0.4757 (m-30) cc_final: 0.3675 (t70) REVERT: B 38 ILE cc_start: 0.7576 (mt) cc_final: 0.7113 (mm) REVERT: B 50 ASN cc_start: 0.8288 (t0) cc_final: 0.8007 (t0) REVERT: B 80 MET cc_start: 0.6316 (tpp) cc_final: 0.5720 (tpt) REVERT: B 519 TRP cc_start: 0.6361 (m-10) cc_final: 0.6068 (m-10) REVERT: B 540 ARG cc_start: 0.6878 (pmt-80) cc_final: 0.6256 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.0529 time to fit residues: 6.6794 Evaluate side-chains 65 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN ** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.153578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.130953 restraints weight = 13290.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.132899 restraints weight = 9956.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.134337 restraints weight = 7994.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.135309 restraints weight = 6807.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.135865 restraints weight = 6065.470| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 1.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5360 Z= 0.106 Angle : 0.721 8.004 7436 Z= 0.320 Chirality : 0.053 0.361 867 Planarity : 0.006 0.105 807 Dihedral : 14.999 159.523 1057 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.22 % Allowed : 0.66 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.21 (0.37), residues: 548 helix: 0.97 (0.33), residues: 271 sheet: 0.32 (0.74), residues: 56 loop : -0.91 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 552 TYR 0.013 0.001 TYR B 391 PHE 0.009 0.001 PHE B 168 TRP 0.009 0.001 TRP A 620 HIS 0.003 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 5360) covalent geometry : angle 0.72119 / 0.32 ( 7436) hydrogen bonds : bond 0.03180 / 2.14 ( 218) hydrogen bonds : angle 4.21521 / 2.97 ( 616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1015.92 seconds wall clock time: 18 minutes 27.01 seconds (1107.01 seconds total)