Starting phenix.real_space_refine on Tue Feb 11 11:52:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7slp_25197/02_2025/7slp_25197.cif Found real_map, /net/cci-nas-00/data/ceres_data/7slp_25197/02_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_25197/02_2025/7slp_25197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7slp_25197/02_2025/7slp_25197.map" model { file = "/net/cci-nas-00/data/ceres_data/7slp_25197/02_2025/7slp_25197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7slp_25197/02_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-5592/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: 3.95, per 1000 atoms: 0.76 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: 1.42 Conformation dependent library (CDL) restraints added in 691.6 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: 1.71 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: 1.78 Time building geometry restraints manager: 1.63 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: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 0.040 Set scattering table: 0.050 Process input model: 17.530 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.070 ------------------------------------------------------------------------------- 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 : 0.541 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: 0.1868 time to fit residues: 36.7599 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 : 0.511 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.155309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.131177 restraints weight = 11989.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.133875 restraints weight = 8010.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.135772 restraints weight = 6078.215| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 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 : 0.569 Fit side-chains revert: symmetry clash REVERT: A 449 ASP cc_start: 0.7502 (t0) cc_final: 0.7119 (t0) REVERT: A 582 SER cc_start: 0.7171 (m) cc_final: 0.6785 (t) REVERT: B 50 ASN cc_start: 0.7864 (t0) cc_final: 0.7645 (t0) REVERT: B 77 PHE cc_start: 0.7589 (m-10) cc_final: 0.7330 (m-80) REVERT: B 80 MET cc_start: 0.5792 (tpt) cc_final: 0.5060 (tpt) REVERT: B 408 GLN cc_start: 0.7073 (tm-30) cc_final: 0.6846 (mt0) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1974 time to fit residues: 27.5561 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 : 0.568 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 5 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS B 517 HIS B 530 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.155730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.132316 restraints weight = 11937.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.134502 restraints weight = 8637.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.135798 restraints weight = 6888.343| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5360 Z= 0.152 Angle : 0.582 8.264 7436 Z= 0.297 Chirality : 0.037 0.135 867 Planarity : 0.006 0.098 807 Dihedral : 18.940 102.159 1201 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: -0.68 (0.34), residues: 548 helix: 0.15 (0.31), residues: 270 sheet: 0.46 (0.74), residues: 50 loop : -1.33 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 519 HIS 0.006 0.001 HIS B 517 PHE 0.013 0.002 PHE A 523 TYR 0.017 0.001 TYR B 128 ARG 0.004 0.000 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 98 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 528 THR cc_start: 0.9123 (t) cc_final: 0.8801 (m) REVERT: A 542 ASP cc_start: 0.3797 (m-30) cc_final: 0.3496 (m-30) REVERT: A 582 SER cc_start: 0.7085 (m) cc_final: 0.6752 (t) REVERT: B 80 MET cc_start: 0.5576 (tpt) cc_final: 0.4887 (tpt) REVERT: B 154 ILE cc_start: 0.8688 (mt) cc_final: 0.8443 (mp) REVERT: B 408 GLN cc_start: 0.7271 (tm-30) cc_final: 0.6976 (mt0) REVERT: B 540 ARG cc_start: 0.5688 (ppt170) cc_final: 0.5186 (ptm160) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1549 time to fit residues: 20.0779 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 : 0.544 ------------------------------------------------------------------------------- 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: 7.9990 chunk 4 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 2 optimal weight: 0.0010 chunk 47 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 43 optimal weight: 0.0770 chunk 5 optimal weight: 3.9990 overall best weight: 1.1346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.154333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.129357 restraints weight = 12262.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.131914 restraints weight = 8391.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.133634 restraints weight = 6390.239| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.8202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5360 Z= 0.168 Angle : 0.589 8.340 7436 Z= 0.299 Chirality : 0.038 0.177 867 Planarity : 0.006 0.095 807 Dihedral : 18.674 98.981 1201 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.78 (0.32), residues: 265 sheet: -0.08 (0.72), residues: 54 loop : -0.81 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 586 HIS 0.006 0.001 HIS A 606 PHE 0.012 0.002 PHE A 523 TYR 0.019 0.002 TYR B 128 ARG 0.006 0.000 ARG B 95 *********************** 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 100 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: B 45 TRP cc_start: 0.8854 (m-10) cc_final: 0.8632 (m-10) REVERT: B 80 MET cc_start: 0.6550 (tpt) cc_final: 0.6022 (tpt) REVERT: B 401 SER cc_start: 0.8392 (m) cc_final: 0.8148 (p) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1494 time to fit residues: 19.8493 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 : 0.549 ------------------------------------------------------------------------------- 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: 6.9990 chunk 56 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 456 HIS ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.148730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.126064 restraints weight = 12793.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.126549 restraints weight = 11436.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.127429 restraints weight = 9321.320| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 1.0533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5360 Z= 0.311 Angle : 0.787 8.952 7436 Z= 0.409 Chirality : 0.045 0.146 867 Planarity : 0.007 0.101 807 Dihedral : 19.591 97.667 1201 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.35), residues: 548 helix: -0.02 (0.30), residues: 271 sheet: -0.27 (0.69), residues: 57 loop : -1.23 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 384 HIS 0.007 0.002 HIS A 606 PHE 0.020 0.003 PHE B 44 TYR 0.019 0.002 TYR A 604 ARG 0.016 0.001 ARG B 540 *********************** 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 : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 ASP cc_start: 0.7491 (t0) cc_final: 0.7126 (t0) REVERT: B 383 GLU cc_start: 0.6753 (tt0) cc_final: 0.6527 (tt0) REVERT: B 564 ILE cc_start: 0.9116 (tp) cc_final: 0.8848 (mm) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1568 time to fit residues: 18.6442 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 : 0.544 ------------------------------------------------------------------------------- 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: 0.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.150294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.127214 restraints weight = 12799.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.129283 restraints weight = 9416.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.130731 restraints weight = 7573.927| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 1.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5360 Z= 0.219 Angle : 0.635 8.436 7436 Z= 0.328 Chirality : 0.040 0.133 867 Planarity : 0.006 0.099 807 Dihedral : 19.020 95.931 1201 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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 (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: -0.42 (0.35), residues: 548 helix: 0.53 (0.32), residues: 270 sheet: 0.13 (0.80), residues: 48 loop : -1.30 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 586 HIS 0.007 0.001 HIS A 606 PHE 0.011 0.002 PHE B 77 TYR 0.013 0.002 TYR A 575 ARG 0.004 0.000 ARG A 484 *********************** 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 89 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 ASP cc_start: 0.7792 (t0) cc_final: 0.7456 (t0) REVERT: B 80 MET cc_start: 0.7268 (tpp) cc_final: 0.6656 (tpt) REVERT: B 145 PHE cc_start: 0.7748 (m-10) cc_final: 0.7466 (m-80) REVERT: B 519 TRP cc_start: 0.6399 (m-10) cc_final: 0.6129 (m-10) REVERT: B 564 ILE cc_start: 0.9157 (tp) cc_final: 0.8871 (mm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1533 time to fit residues: 18.3244 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 : 0.514 ------------------------------------------------------------------------------- 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: 6.9990 chunk 22 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 158 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.148554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.125182 restraints weight = 12947.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.127037 restraints weight = 9804.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.128499 restraints weight = 7994.391| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 1.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5360 Z= 0.252 Angle : 0.674 8.164 7436 Z= 0.344 Chirality : 0.041 0.155 867 Planarity : 0.006 0.107 807 Dihedral : 19.041 95.206 1201 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.22 % Allowed : 0.88 % 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: -0.47 (0.36), residues: 548 helix: 0.55 (0.32), residues: 269 sheet: 0.05 (0.76), residues: 50 loop : -1.41 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 384 HIS 0.007 0.002 HIS A 606 PHE 0.013 0.002 PHE B 44 TYR 0.014 0.002 TYR A 575 ARG 0.003 0.001 ARG A 443 *********************** 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 86 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 476 ASP cc_start: 0.6767 (t70) cc_final: 0.6507 (t70) REVERT: B 84 THR cc_start: 0.6624 (m) cc_final: 0.6416 (m) REVERT: B 519 TRP cc_start: 0.6380 (m-10) cc_final: 0.6043 (m-10) REVERT: B 564 ILE cc_start: 0.9114 (tp) cc_final: 0.8825 (mm) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1298 time to fit residues: 15.3815 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 : 0.547 ------------------------------------------------------------------------------- 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: 20.0000 chunk 20 optimal weight: 0.0370 chunk 5 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.151748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.128610 restraints weight = 13057.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.130724 restraints weight = 9599.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.132207 restraints weight = 7664.985| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 1.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5360 Z= 0.158 Angle : 0.576 7.490 7436 Z= 0.290 Chirality : 0.038 0.128 867 Planarity : 0.006 0.109 807 Dihedral : 18.732 94.284 1201 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.12 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: -0.10 (0.36), residues: 548 helix: 0.99 (0.33), residues: 263 sheet: 0.04 (0.76), residues: 50 loop : -1.31 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 384 HIS 0.004 0.001 HIS A 489 PHE 0.012 0.002 PHE A 647 TYR 0.019 0.002 TYR A 661 ARG 0.003 0.000 ARG A 478 *********************** 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 83 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 579 LEU cc_start: 0.8008 (tp) cc_final: 0.7738 (tp) REVERT: B 540 ARG cc_start: 0.7142 (pmt-80) cc_final: 0.6297 (ptm-80) REVERT: B 564 ILE cc_start: 0.9097 (tp) cc_final: 0.8837 (mm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1298 time to fit residues: 15.1107 Evaluate side-chains 66 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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: 0.8980 chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS ** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.153199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.130043 restraints weight = 12928.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.132197 restraints weight = 9555.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.133443 restraints weight = 7617.241| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 1.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5360 Z= 0.150 Angle : 0.566 7.489 7436 Z= 0.279 Chirality : 0.037 0.129 867 Planarity : 0.006 0.107 807 Dihedral : 18.487 94.122 1201 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 0.09 (0.36), residues: 548 helix: 1.15 (0.33), residues: 269 sheet: 0.25 (0.76), residues: 50 loop : -1.32 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 384 HIS 0.004 0.001 HIS A 606 PHE 0.009 0.001 PHE B 77 TYR 0.011 0.001 TYR A 604 ARG 0.002 0.000 ARG B 143 *********************** 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: 0 poor density : 82 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: B 38 ILE cc_start: 0.7714 (mt) cc_final: 0.7230 (mm) REVERT: B 540 ARG cc_start: 0.7277 (pmt-80) cc_final: 0.6418 (ptm-80) REVERT: B 564 ILE cc_start: 0.9007 (tp) cc_final: 0.8727 (mm) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1341 time to fit residues: 15.3547 Evaluate side-chains 66 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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: 7.9990 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 0.0670 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 HIS A 682 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.155484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.132865 restraints weight = 13242.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.134950 restraints weight = 9685.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.136179 restraints weight = 7736.878| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 1.2340 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= 0.141 Angle : 0.544 7.127 7436 Z= 0.270 Chirality : 0.037 0.128 867 Planarity : 0.006 0.103 807 Dihedral : 18.313 93.250 1201 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: 0.34 (0.36), residues: 548 helix: 1.34 (0.33), residues: 269 sheet: 0.55 (0.77), residues: 50 loop : -1.21 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 533 HIS 0.010 0.001 HIS A 682 PHE 0.014 0.001 PHE A 647 TYR 0.013 0.001 TYR B 128 ARG 0.002 0.000 ARG A 484 ********************** 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 86 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LEU cc_start: 0.8060 (tp) cc_final: 0.7789 (tp) REVERT: B 38 ILE cc_start: 0.7656 (mt) cc_final: 0.7199 (mm) REVERT: B 80 MET cc_start: 0.6682 (tpp) cc_final: 0.6197 (tpt) REVERT: B 540 ARG cc_start: 0.7117 (pmt-80) cc_final: 0.6449 (ptm-80) REVERT: B 564 ILE cc_start: 0.8979 (tp) cc_final: 0.8714 (mm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1288 time to fit residues: 15.6113 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 : 0.513 ------------------------------------------------------------------------------- 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: 6.9990 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 10 optimal weight: 0.0070 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.150903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.127830 restraints weight = 13489.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.129773 restraints weight = 10154.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.131179 restraints weight = 8205.157| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 1.2587 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= 0.207 Angle : 0.613 6.728 7436 Z= 0.306 Chirality : 0.039 0.149 867 Planarity : 0.006 0.101 807 Dihedral : 18.477 93.515 1201 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.63 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: 0.11 (0.37), residues: 548 helix: 1.05 (0.33), residues: 270 sheet: 0.42 (0.77), residues: 52 loop : -1.21 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 519 HIS 0.006 0.001 HIS A 606 PHE 0.010 0.001 PHE B 77 TYR 0.012 0.002 TYR A 623 ARG 0.003 0.000 ARG A 484 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1717.51 seconds wall clock time: 31 minutes 38.35 seconds (1898.35 seconds total)