Starting phenix.real_space_refine on Thu Mar 6 08:32:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7slp_25197/03_2025/7slp_25197.cif Found real_map, /net/cci-nas-00/data/ceres_data/7slp_25197/03_2025/7slp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7slp_25197/03_2025/7slp_25197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7slp_25197/03_2025/7slp_25197.map" model { file = "/net/cci-nas-00/data/ceres_data/7slp_25197/03_2025/7slp_25197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7slp_25197/03_2025/7slp_25197.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP: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: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 2} 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: 4.04, per 1000 atoms: 0.78 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: 1.37 Conformation dependent library (CDL) restraints added in 707.3 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 49.7% alpha, 11.4% beta 8 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 1.82 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: 1.66 Time building geometry restraints manager: 1.64 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: 2895 21.54 - 43.07: 262 43.07 - 64.60: 88 64.60 - 86.14: 24 86.14 - 107.67: 7 Dihedral angle restraints: 3276 sinusoidal: 1641 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 3273 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: 0.010 Normalize map: mean=0, sd=1: 0.510 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 18.470 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5588 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= 0.513 Angle : 1.220 10.794 7436 Z= 0.688 Chirality : 0.067 0.432 867 Planarity : 0.008 0.065 807 Dihedral : 19.399 107.672 2218 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.003 TRP B 384 HIS 0.009 0.003 HIS B 494 PHE 0.033 0.004 PHE A 442 TYR 0.029 0.005 TYR A 661 ARG 0.010 0.001 ARG A 484 *********************** 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 : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.7271 (ttt) cc_final: 0.6914 (tmm) REVERT: A 538 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7808 (mt0) REVERT: A 557 THR cc_start: 0.6231 (t) cc_final: 0.5925 (t) REVERT: A 582 SER cc_start: 0.6965 (m) cc_final: 0.6745 (t) REVERT: A 607 LEU cc_start: 0.5854 (mt) cc_final: 0.5630 (mp) REVERT: A 661 TYR cc_start: 0.6298 (p90) cc_final: 0.6022 (p90) REVERT: B 50 ASN cc_start: 0.7391 (t0) cc_final: 0.7135 (t0) REVERT: B 123 ASP cc_start: 0.8371 (t0) cc_final: 0.8167 (t0) REVERT: B 159 TYR cc_start: 0.6892 (m-80) cc_final: 0.6437 (m-80) REVERT: B 459 ILE cc_start: 0.7413 (mt) cc_final: 0.7138 (tt) outliers start: 8 outliers final: 4 residues processed: 158 average time/residue: 0.1943 time to fit residues: 38.2267 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 : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 0.0370 chunk 52 optimal weight: 3.9990 overall best weight: 1.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4118 r_free = 0.4118 target = 0.154798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.133015 restraints weight = 12021.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.132980 restraints weight = 9666.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.133663 restraints weight = 8484.912| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5360 Z= 0.245 Angle : 0.725 8.916 7436 Z= 0.370 Chirality : 0.039 0.145 867 Planarity : 0.007 0.080 807 Dihedral : 19.385 102.550 1201 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.32), residues: 548 helix: -0.86 (0.29), residues: 261 sheet: -0.22 (0.60), residues: 69 loop : -1.41 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 586 HIS 0.008 0.002 HIS A 588 PHE 0.020 0.003 PHE B 44 TYR 0.017 0.002 TYR A 415 ARG 0.007 0.001 ARG A 626 *********************** 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 111 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 449 ASP cc_start: 0.7285 (t0) cc_final: 0.6962 (t0) REVERT: A 582 SER cc_start: 0.7048 (m) cc_final: 0.6704 (t) REVERT: B 77 PHE cc_start: 0.7393 (m-10) cc_final: 0.7165 (m-80) REVERT: B 80 MET cc_start: 0.5633 (tpt) cc_final: 0.4869 (tpt) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1999 time to fit residues: 27.8323 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 : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 5 optimal weight: 0.0980 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 HIS B 408 GLN B 517 HIS B 530 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.153149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129055 restraints weight = 11984.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.131176 restraints weight = 8889.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.132660 restraints weight = 7118.203| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.7597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5360 Z= 0.214 Angle : 0.659 8.373 7436 Z= 0.338 Chirality : 0.039 0.142 867 Planarity : 0.007 0.097 807 Dihedral : 19.161 103.633 1201 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.34), residues: 548 helix: 0.02 (0.31), residues: 266 sheet: -0.23 (0.74), residues: 50 loop : -1.09 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 519 HIS 0.008 0.002 HIS A 606 PHE 0.017 0.002 PHE A 523 TYR 0.017 0.002 TYR B 128 ARG 0.008 0.001 ARG A 626 *********************** 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 : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 600 PHE cc_start: 0.7670 (m-10) cc_final: 0.7408 (m-80) REVERT: B 80 MET cc_start: 0.5943 (tpt) cc_final: 0.5494 (tpt) REVERT: B 154 ILE cc_start: 0.8982 (mt) cc_final: 0.8744 (mp) REVERT: B 383 GLU cc_start: 0.6603 (tt0) cc_final: 0.6361 (tt0) REVERT: B 401 SER cc_start: 0.8117 (m) cc_final: 0.7879 (p) REVERT: B 540 ARG cc_start: 0.6089 (ppt170) cc_final: 0.5842 (ptm160) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1611 time to fit residues: 21.8673 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 : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.149947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.124887 restraints weight = 12371.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.127402 restraints weight = 8453.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.129174 restraints weight = 6480.361| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.9464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5360 Z= 0.247 Angle : 0.674 7.647 7436 Z= 0.347 Chirality : 0.041 0.129 867 Planarity : 0.006 0.092 807 Dihedral : 19.136 98.284 1201 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.35), residues: 548 helix: 0.18 (0.31), residues: 271 sheet: -0.28 (0.71), residues: 50 loop : -1.15 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 586 HIS 0.008 0.002 HIS A 606 PHE 0.021 0.002 PHE A 523 TYR 0.021 0.002 TYR A 604 ARG 0.006 0.001 ARG B 552 *********************** 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 94 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 LEU cc_start: 0.5829 (mt) cc_final: 0.4508 (mp) REVERT: B 128 TYR cc_start: 0.8448 (t80) cc_final: 0.8068 (t80) REVERT: B 394 LEU cc_start: 0.9005 (mt) cc_final: 0.8586 (mm) REVERT: B 401 SER cc_start: 0.8538 (m) cc_final: 0.8326 (p) REVERT: B 540 ARG cc_start: 0.6705 (ppt170) cc_final: 0.6324 (ptm160) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1590 time to fit residues: 19.9022 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 : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.151525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.128605 restraints weight = 12842.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.130695 restraints weight = 9426.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.132234 restraints weight = 7535.540| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 1.0475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5360 Z= 0.206 Angle : 0.613 8.579 7436 Z= 0.313 Chirality : 0.039 0.151 867 Planarity : 0.006 0.095 807 Dihedral : 18.969 95.133 1201 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.36), residues: 548 helix: 0.47 (0.32), residues: 272 sheet: -0.94 (0.63), residues: 59 loop : -1.00 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 519 HIS 0.008 0.002 HIS A 606 PHE 0.012 0.002 PHE B 44 TYR 0.015 0.002 TYR B 128 ARG 0.005 0.000 ARG B 552 *********************** 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 90 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 MET cc_start: 0.6885 (tpp) cc_final: 0.6592 (tpt) REVERT: B 540 ARG cc_start: 0.6599 (ppt170) cc_final: 0.6351 (ptm160) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1426 time to fit residues: 17.3241 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 : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 53 optimal weight: 0.3980 chunk 1 optimal weight: 0.0670 chunk 52 optimal weight: 0.6980 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS ** A 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 408 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.153725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.130928 restraints weight = 13073.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.133000 restraints weight = 9603.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.134452 restraints weight = 7700.345| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 1.0921 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= 0.142 Angle : 0.547 8.105 7436 Z= 0.275 Chirality : 0.038 0.136 867 Planarity : 0.005 0.095 807 Dihedral : 18.566 94.986 1201 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.36), residues: 548 helix: 0.92 (0.32), residues: 270 sheet: -0.24 (0.72), residues: 53 loop : -0.96 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 519 HIS 0.004 0.001 HIS A 606 PHE 0.007 0.001 PHE A 647 TYR 0.011 0.001 TYR B 391 ARG 0.008 0.001 ARG B 552 *********************** 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 92 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8594 (tppp) cc_final: 0.8171 (tptt) REVERT: B 80 MET cc_start: 0.7156 (tpp) cc_final: 0.6469 (tpt) REVERT: B 390 GLU cc_start: 0.7888 (pp20) cc_final: 0.7348 (pp20) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1574 time to fit residues: 19.3272 Evaluate side-chains 71 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 12 optimal weight: 0.8980 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 481 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 408 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.150424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.126300 restraints weight = 12654.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.128896 restraints weight = 8712.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.130698 restraints weight = 6651.808| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 1.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5360 Z= 0.191 Angle : 0.589 8.287 7436 Z= 0.294 Chirality : 0.039 0.129 867 Planarity : 0.006 0.102 807 Dihedral : 18.633 94.261 1201 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.37), residues: 548 helix: 0.91 (0.33), residues: 270 sheet: -0.03 (0.74), residues: 55 loop : -1.01 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 45 HIS 0.007 0.001 HIS A 606 PHE 0.013 0.002 PHE A 523 TYR 0.013 0.002 TYR B 532 ARG 0.002 0.000 ARG B 552 *********************** 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 89 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 ASP cc_start: 0.8110 (t0) cc_final: 0.7897 (t0) REVERT: B 80 MET cc_start: 0.7263 (tpp) cc_final: 0.6691 (tpt) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.1498 time to fit residues: 17.6057 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 : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 29 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 481 HIS ** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4102 r_free = 0.4102 target = 0.152110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.127826 restraints weight = 12676.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.130515 restraints weight = 8668.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.132190 restraints weight = 6550.788| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 1.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5360 Z= 0.144 Angle : 0.542 7.373 7436 Z= 0.270 Chirality : 0.037 0.128 867 Planarity : 0.006 0.105 807 Dihedral : 18.386 94.343 1201 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.37), residues: 548 helix: 1.16 (0.33), residues: 270 sheet: 0.02 (0.76), residues: 53 loop : -0.95 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 519 HIS 0.004 0.001 HIS A 606 PHE 0.007 0.001 PHE B 77 TYR 0.011 0.001 TYR B 128 ARG 0.004 0.000 ARG B 143 *********************** 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 87 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 LYS cc_start: 0.8505 (ttmt) cc_final: 0.8056 (tptt) REVERT: B 80 MET cc_start: 0.7224 (tpp) cc_final: 0.6697 (tpt) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1592 time to fit residues: 18.7867 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 : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 408 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.148996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.125914 restraints weight = 12959.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.127734 restraints weight = 9841.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.129228 restraints weight = 8035.224| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 1.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5360 Z= 0.220 Angle : 0.616 7.595 7436 Z= 0.308 Chirality : 0.039 0.133 867 Planarity : 0.006 0.104 807 Dihedral : 18.626 94.577 1201 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.22 % Allowed : 1.55 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.36), residues: 548 helix: 1.02 (0.32), residues: 270 sheet: -0.36 (0.73), residues: 57 loop : -1.13 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 384 HIS 0.008 0.001 HIS A 606 PHE 0.014 0.002 PHE B 77 TYR 0.014 0.002 TYR B 532 ARG 0.003 0.000 ARG A 484 *********************** 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 82 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 MET cc_start: 0.6981 (tpp) cc_final: 0.6441 (tpt) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.1449 time to fit residues: 16.1845 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 : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 43 optimal weight: 0.2980 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 0.0870 chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.151387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.127193 restraints weight = 13029.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.129782 restraints weight = 9081.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.131553 restraints weight = 6971.906| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 1.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5360 Z= 0.158 Angle : 0.579 11.629 7436 Z= 0.281 Chirality : 0.038 0.126 867 Planarity : 0.006 0.101 807 Dihedral : 18.445 95.209 1201 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.37), residues: 548 helix: 1.03 (0.33), residues: 271 sheet: -0.28 (0.73), residues: 55 loop : -1.05 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 519 HIS 0.005 0.001 HIS A 606 PHE 0.012 0.001 PHE B 77 TYR 0.013 0.001 TYR B 391 ARG 0.004 0.000 ARG A 478 ********************** 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 87 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 MET cc_start: 0.6881 (tpp) cc_final: 0.6444 (tpt) REVERT: B 540 ARG cc_start: 0.5960 (ttp80) cc_final: 0.5547 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1510 time to fit residues: 17.8728 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 : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.150152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.125569 restraints weight = 13226.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.128227 restraints weight = 9226.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129993 restraints weight = 7044.002| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 1.2555 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= 0.179 Angle : 0.590 9.398 7436 Z= 0.288 Chirality : 0.038 0.127 867 Planarity : 0.006 0.095 807 Dihedral : 18.434 95.489 1201 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.37), residues: 548 helix: 1.09 (0.33), residues: 265 sheet: -0.26 (0.73), residues: 57 loop : -1.13 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 384 HIS 0.006 0.001 HIS A 606 PHE 0.011 0.001 PHE B 44 TYR 0.011 0.001 TYR B 532 ARG 0.003 0.000 ARG A 478 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1813.57 seconds wall clock time: 32 minutes 10.54 seconds (1930.54 seconds total)