Starting phenix.real_space_refine on Thu Jul 2 01:52:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7slp_25197/07_2026/7slp_25197.cif Found real_map, /net/cci-nas-00/data/ceres_data/7slp_25197/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7slp_25197/07_2026/7slp_25197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7slp_25197/07_2026/7slp_25197.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7slp_25197/07_2026/7slp_25197.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7slp_25197/07_2026/7slp_25197.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7slp_25197/07_2026/7slp_25197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7slp_25197/07_2026/7slp_25197.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNA': 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: 1.18, per 1000 atoms: 0.23 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: 0.44 Conformation dependent library (CDL) restraints added in 159.4 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: 0.44 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: 0.46 Time building geometry restraints manager: 0.58 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: 6922 2.16 - 4.32: 427 4.32 - 6.48: 62 6.48 - 8.64: 16 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=" C4' G R 300 " pdb=" C3' G R 300 " pdb=" O3' G R 300 " ideal model delta sigma weight residual 109.40 119.08 -9.68 1.50e+00 4.44e-01 4.16e+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 ... (remaining 7431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 2833 21.54 - 43.07: 231 43.07 - 64.60: 48 64.60 - 86.14: 13 86.14 - 107.67: 7 Dihedral angle restraints: 3132 sinusoidal: 1497 harmonic: 1635 Sorted by residual: dihedral pdb=" CA ASN A 426 " pdb=" C ASN A 426 " pdb=" N PRO A 427 " pdb=" CA PRO A 427 " ideal model delta harmonic sigma weight residual 180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA HIS A 682 " pdb=" C HIS A 682 " pdb=" N LYS A 683 " pdb=" CA LYS A 683 " ideal model delta harmonic sigma weight residual 180.00 156.21 23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ARG B 55 " pdb=" C ARG B 55 " pdb=" N PHE B 56 " pdb=" CA PHE B 56 " ideal model delta harmonic sigma weight residual -180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 3129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 733 0.086 - 0.173: 115 0.173 - 0.259: 16 0.259 - 0.345: 1 0.345 - 0.432: 2 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=" CA PHE A 523 " pdb=" N PHE A 523 " pdb=" C PHE A 523 " pdb=" CB PHE A 523 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA LEU B 131 " pdb=" N LEU B 131 " pdb=" C LEU B 131 " pdb=" CB LEU B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+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: 0.470 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.920 Find NCS groups from input model: 0.010 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.300 ------------------------------------------------------------------------------- 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= 0.413 Angle : 1.220 10.794 7436 Z= 0.688 Chirality : 0.067 0.432 867 Planarity : 0.008 0.065 807 Dihedral : 17.077 107.672 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 0.00820 / 0.41 ( 5360) covalent geometry : angle 1.21981 / 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 : 0.121 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: 0.0687 time to fit residues: 13.7124 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 : 0.119 ------------------------------------------------------------------------------- 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: 5.9990 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.155950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.132644 restraints weight = 12142.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.135085 restraints weight = 8512.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.136779 restraints weight = 6658.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.137845 restraints weight = 5559.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.138683 restraints weight = 4942.724| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5360 Z= 0.170 Angle : 0.702 9.089 7436 Z= 0.358 Chirality : 0.039 0.142 867 Planarity : 0.007 0.081 807 Dihedral : 14.631 101.338 1057 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % 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: -1.61 (0.32), residues: 548 helix: -0.86 (0.29), residues: 259 sheet: -0.32 (0.69), residues: 50 loop : -1.34 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 626 TYR 0.015 0.002 TYR A 650 PHE 0.018 0.002 PHE B 44 TRP 0.033 0.003 TRP A 586 HIS 0.007 0.002 HIS A 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 5360) covalent geometry : angle 0.70220 / 0.36 ( 7436) hydrogen bonds : bond 0.04820 / 3.21 ( 218) hydrogen bonds : angle 5.26146 / 3.67 ( 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 : 0.128 Fit side-chains revert: symmetry clash REVERT: A 449 ASP cc_start: 0.7191 (t0) cc_final: 0.6852 (t0) REVERT: A 452 CYS cc_start: 0.7750 (p) cc_final: 0.6375 (t) REVERT: A 582 SER cc_start: 0.7092 (m) cc_final: 0.6776 (t) REVERT: A 608 ARG cc_start: 0.7589 (mtp85) cc_final: 0.7213 (ptp-170) REVERT: B 38 ILE cc_start: 0.7306 (mt) cc_final: 0.7070 (mt) REVERT: B 80 MET cc_start: 0.5557 (tpt) cc_final: 0.4776 (tpt) REVERT: B 540 ARG cc_start: 0.5347 (ppt170) cc_final: 0.4923 (ptm160) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0716 time to fit residues: 10.2885 Evaluate side-chains 72 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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: 7.9990 chunk 52 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 456 HIS B 50 ASN B 408 GLN B 530 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.151548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.127421 restraints weight = 12020.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.129438 restraints weight = 9001.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.130881 restraints weight = 7340.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.131694 restraints weight = 6301.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.132393 restraints weight = 5725.607| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.8303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5360 Z= 0.202 Angle : 0.759 7.980 7436 Z= 0.393 Chirality : 0.042 0.162 867 Planarity : 0.007 0.090 807 Dihedral : 14.652 106.364 1057 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % 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: -0.98 (0.34), residues: 548 helix: -0.10 (0.30), residues: 264 sheet: -0.60 (0.72), residues: 50 loop : -1.20 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 626 TYR 0.023 0.002 TYR A 490 PHE 0.026 0.003 PHE A 523 TRP 0.039 0.003 TRP A 441 HIS 0.010 0.002 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 ( 5360) covalent geometry : angle 0.75921 / 0.39 ( 7436) hydrogen bonds : bond 0.05363 / 3.47 ( 218) hydrogen bonds : angle 5.45106 / 3.77 ( 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 109 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 608 ARG cc_start: 0.7342 (mtp85) cc_final: 0.6803 (ptp-170) REVERT: B 128 TYR cc_start: 0.8248 (t80) cc_final: 0.7854 (t80) REVERT: B 154 ILE cc_start: 0.9032 (mt) cc_final: 0.8773 (mp) REVERT: B 540 ARG cc_start: 0.6126 (ppt170) cc_final: 0.5365 (ptm160) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0621 time to fit residues: 8.9685 Evaluate side-chains 72 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 453 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.142976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.116843 restraints weight = 12827.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.118982 restraints weight = 9323.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.120562 restraints weight = 7477.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.121569 restraints weight = 6393.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.122413 restraints weight = 5726.014| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 1.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 5360 Z= 0.305 Angle : 0.899 9.260 7436 Z= 0.464 Chirality : 0.047 0.172 867 Planarity : 0.007 0.095 807 Dihedral : 15.573 99.396 1057 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % 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: -1.76 (0.32), residues: 548 helix: -0.55 (0.29), residues: 268 sheet: -0.78 (0.55), residues: 67 loop : -1.99 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 484 TYR 0.021 0.003 TYR A 604 PHE 0.032 0.004 PHE B 44 TRP 0.027 0.003 TRP B 519 HIS 0.011 0.003 HIS A 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.30 ( 5360) covalent geometry : angle 0.89854 / 0.46 ( 7436) hydrogen bonds : bond 0.06723 / 4.50 ( 218) hydrogen bonds : angle 6.40686 / 4.40 ( 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 83 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.6870 (mtp) cc_final: 0.6382 (ttm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0630 time to fit residues: 6.8191 Evaluate side-chains 55 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.148335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.124213 restraints weight = 12906.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.126351 restraints weight = 9511.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.127729 restraints weight = 7648.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.128875 restraints weight = 6559.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.129670 restraints weight = 5876.542| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 1.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5360 Z= 0.145 Angle : 0.638 8.414 7436 Z= 0.324 Chirality : 0.040 0.139 867 Planarity : 0.005 0.081 807 Dihedral : 14.279 94.842 1057 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -0.86 (0.35), residues: 548 helix: 0.32 (0.31), residues: 269 sheet: -0.37 (0.77), residues: 48 loop : -1.67 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 472 TYR 0.018 0.002 TYR A 661 PHE 0.020 0.002 PHE A 523 TRP 0.012 0.002 TRP B 384 HIS 0.008 0.001 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 5360) covalent geometry : angle 0.63782 / 0.32 ( 7436) hydrogen bonds : bond 0.04172 / 2.85 ( 218) hydrogen bonds : angle 5.09333 / 3.55 ( 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 89 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 ASN cc_start: 0.8167 (p0) cc_final: 0.7915 (p0) REVERT: A 593 ASP cc_start: 0.4346 (m-30) cc_final: 0.3206 (t70) REVERT: B 80 MET cc_start: 0.7177 (tpp) cc_final: 0.6676 (tpt) REVERT: B 131 LEU cc_start: 0.6923 (tt) cc_final: 0.6682 (tp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0555 time to fit residues: 6.7075 Evaluate side-chains 63 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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: 10.0000 chunk 56 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 7 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.149916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124397 restraints weight = 12694.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126992 restraints weight = 8876.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.128833 restraints weight = 6845.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130219 restraints weight = 5670.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.130970 restraints weight = 4939.848| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 1.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5360 Z= 0.113 Angle : 0.588 8.497 7436 Z= 0.292 Chirality : 0.037 0.133 867 Planarity : 0.005 0.098 807 Dihedral : 13.667 95.519 1057 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: -0.34 (0.36), residues: 548 helix: 0.87 (0.32), residues: 269 sheet: -0.23 (0.78), residues: 48 loop : -1.55 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 472 TYR 0.014 0.001 TYR A 575 PHE 0.015 0.002 PHE A 523 TRP 0.014 0.001 TRP B 384 HIS 0.005 0.001 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 5360) covalent geometry : angle 0.58823 / 0.29 ( 7436) hydrogen bonds : bond 0.03733 / 2.51 ( 218) hydrogen bonds : angle 4.68255 / 3.28 ( 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 84 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 614 VAL cc_start: 0.8167 (m) cc_final: 0.7944 (m) REVERT: A 615 LEU cc_start: 0.6490 (mt) cc_final: 0.5101 (mp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0531 time to fit residues: 6.0368 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 : 0.133 ------------------------------------------------------------------------------- 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: 9.9990 chunk 31 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 0.1980 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.142655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.117102 restraints weight = 13228.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.119412 restraints weight = 9527.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.120736 restraints weight = 7519.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.122099 restraints weight = 6444.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.122806 restraints weight = 5738.384| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 1.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 5360 Z= 0.277 Angle : 0.816 8.491 7436 Z= 0.414 Chirality : 0.044 0.161 867 Planarity : 0.007 0.109 807 Dihedral : 14.931 96.413 1057 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: -1.09 (0.35), residues: 548 helix: 0.15 (0.31), residues: 268 sheet: -0.24 (0.67), residues: 58 loop : -1.92 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 484 TYR 0.024 0.003 TYR A 623 PHE 0.023 0.003 PHE B 44 TRP 0.022 0.003 TRP B 384 HIS 0.011 0.002 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.28 ( 5360) covalent geometry : angle 0.81562 / 0.41 ( 7436) hydrogen bonds : bond 0.05727 / 3.84 ( 218) hydrogen bonds : angle 5.57257 / 3.88 ( 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 73 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.151 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0588 time to fit residues: 5.8190 Evaluate side-chains 51 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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: 0.0570 chunk 18 optimal weight: 0.0020 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.6110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN A 481 HIS ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS B 408 GLN B 546 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.150927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.125849 restraints weight = 12947.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.128439 restraints weight = 8984.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.130319 restraints weight = 6916.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.131334 restraints weight = 5706.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.132466 restraints weight = 5071.431| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 1.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5360 Z= 0.106 Angle : 0.597 10.021 7436 Z= 0.295 Chirality : 0.038 0.147 867 Planarity : 0.006 0.092 807 Dihedral : 13.821 95.756 1057 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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: -0.40 (0.36), residues: 548 helix: 0.87 (0.32), residues: 270 sheet: -0.42 (0.77), residues: 49 loop : -1.63 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 531 TYR 0.012 0.001 TYR B 391 PHE 0.011 0.002 PHE A 658 TRP 0.009 0.001 TRP A 586 HIS 0.007 0.001 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 5360) covalent geometry : angle 0.59677 / 0.30 ( 7436) hydrogen bonds : bond 0.03742 / 2.52 ( 218) hydrogen bonds : angle 4.73620 / 3.31 ( 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 84 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.7778 (mt) cc_final: 0.7426 (mm) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.0531 time to fit residues: 5.9676 Evaluate side-chains 63 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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: 5.9990 chunk 22 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN A 606 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.147364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.121971 restraints weight = 13088.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.124304 restraints weight = 9384.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.125773 restraints weight = 7371.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.127089 restraints weight = 6276.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.127798 restraints weight = 5551.100| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 1.2853 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= 0.150 Angle : 0.641 8.357 7436 Z= 0.320 Chirality : 0.039 0.142 867 Planarity : 0.006 0.101 807 Dihedral : 13.848 96.010 1057 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % 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: -0.49 (0.36), residues: 548 helix: 0.75 (0.33), residues: 270 sheet: -0.37 (0.78), residues: 52 loop : -1.63 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 484 TYR 0.021 0.002 TYR B 128 PHE 0.013 0.002 PHE A 658 TRP 0.016 0.002 TRP B 384 HIS 0.004 0.001 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 5360) covalent geometry : angle 0.64133 / 0.32 ( 7436) hydrogen bonds : bond 0.04118 / 2.78 ( 218) hydrogen bonds : angle 4.84700 / 3.39 ( 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 80 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 540 ARG cc_start: 0.6550 (tmt170) cc_final: 0.5788 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.0485 time to fit residues: 5.4382 Evaluate side-chains 61 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 0.0970 chunk 25 optimal weight: 0.2980 chunk 47 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.149205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.123586 restraints weight = 13178.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.125983 restraints weight = 9385.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.127768 restraints weight = 7347.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.128789 restraints weight = 6139.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.129793 restraints weight = 5455.100| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 1.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5360 Z= 0.119 Angle : 0.592 8.386 7436 Z= 0.294 Chirality : 0.038 0.135 867 Planarity : 0.006 0.096 807 Dihedral : 13.516 95.883 1057 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % 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: -0.33 (0.37), residues: 548 helix: 0.90 (0.33), residues: 270 sheet: -0.44 (0.77), residues: 52 loop : -1.54 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 531 TYR 0.015 0.001 TYR B 391 PHE 0.011 0.002 PHE A 658 TRP 0.021 0.002 TRP B 519 HIS 0.010 0.001 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 5360) covalent geometry : angle 0.59174 / 0.29 ( 7436) hydrogen bonds : bond 0.03728 / 2.48 ( 218) hydrogen bonds : angle 4.67945 / 3.27 ( 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 81 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 540 ARG cc_start: 0.6552 (tmt170) cc_final: 0.5685 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.0458 time to fit residues: 5.0571 Evaluate side-chains 63 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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: 8.9990 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 35 optimal weight: 0.0070 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.152548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127390 restraints weight = 13010.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129830 restraints weight = 9128.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.131687 restraints weight = 7048.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.132695 restraints weight = 5830.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.133762 restraints weight = 5147.653| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 1.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5360 Z= 0.093 Angle : 0.552 8.151 7436 Z= 0.269 Chirality : 0.037 0.133 867 Planarity : 0.005 0.092 807 Dihedral : 12.914 95.311 1057 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % 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: -0.06 (0.37), residues: 548 helix: 1.14 (0.33), residues: 270 sheet: -0.36 (0.75), residues: 53 loop : -1.43 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 531 TYR 0.013 0.001 TYR B 128 PHE 0.008 0.001 PHE A 600 TRP 0.018 0.002 TRP B 519 HIS 0.004 0.001 HIS A 606 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 ( 5360) covalent geometry : angle 0.55218 / 0.27 ( 7436) hydrogen bonds : bond 0.03195 / 2.13 ( 218) hydrogen bonds : angle 4.39289 / 3.09 ( 616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 816.20 seconds wall clock time: 14 minutes 44.66 seconds (884.66 seconds total)