Starting phenix.real_space_refine on Fri Dec 27 15:07:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7slp_25197/12_2024/7slp_25197.cif Found real_map, /net/cci-nas-00/data/ceres_data/7slp_25197/12_2024/7slp_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_25197/12_2024/7slp_25197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7slp_25197/12_2024/7slp_25197.map" model { file = "/net/cci-nas-00/data/ceres_data/7slp_25197/12_2024/7slp_25197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7slp_25197/12_2024/7slp_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-5532/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: 3.84, per 1000 atoms: 0.74 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: 1.49 Conformation dependent library (CDL) restraints added in 843.4 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1058 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 4 sheets defined 49.7% alpha, 11.4% beta 8 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 1.69 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: 1.71 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: 0.840 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.550 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.560 ------------------------------------------------------------------------------- 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 : 0.464 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: 0.1946 time to fit residues: 38.1157 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 : 0.539 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 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 : 0.468 Fit side-chains revert: symmetry clash REVERT: A 449 ASP cc_start: 0.7988 (t0) cc_final: 0.7491 (t0) REVERT: A 582 SER cc_start: 0.7258 (m) cc_final: 0.6815 (t) REVERT: B 50 ASN cc_start: 0.7661 (t0) cc_final: 0.7214 (t0) REVERT: B 75 VAL cc_start: 0.8300 (t) cc_final: 0.8089 (t) REVERT: B 77 PHE cc_start: 0.7914 (m-10) cc_final: 0.7658 (m-80) REVERT: B 80 MET cc_start: 0.5879 (tpt) cc_final: 0.5417 (tpt) REVERT: B 408 GLN cc_start: 0.7081 (tm-30) cc_final: 0.6478 (mt0) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2043 time to fit residues: 28.3783 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 : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 43 optimal weight: 0.0050 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.6572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5360 Z= 0.156 Angle : 0.587 8.427 7436 Z= 0.299 Chirality : 0.038 0.147 867 Planarity : 0.006 0.098 807 Dihedral : 18.965 102.298 1201 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % 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: -0.70 (0.34), residues: 548 helix: 0.16 (0.31), residues: 270 sheet: 0.47 (0.74), residues: 50 loop : -1.38 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 519 HIS 0.005 0.001 HIS A 606 PHE 0.014 0.002 PHE A 523 TYR 0.017 0.001 TYR B 128 ARG 0.005 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 99 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 ASP cc_start: 0.4407 (m-30) cc_final: 0.4142 (m-30) REVERT: A 582 SER cc_start: 0.7231 (m) cc_final: 0.6823 (t) REVERT: B 50 ASN cc_start: 0.7740 (t0) cc_final: 0.7345 (t0) REVERT: B 80 MET cc_start: 0.6152 (tpt) cc_final: 0.5580 (tpt) REVERT: B 154 ILE cc_start: 0.8318 (mt) cc_final: 0.8101 (mp) REVERT: B 184 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7492 (tm-30) REVERT: B 408 GLN cc_start: 0.7281 (tm-30) cc_final: 0.6587 (mt0) REVERT: B 540 ARG cc_start: 0.6148 (ppt170) cc_final: 0.5573 (ptm160) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1481 time to fit residues: 19.5160 Evaluate side-chains 74 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 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 27 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- 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 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 1.0226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5360 Z= 0.376 Angle : 0.858 7.892 7436 Z= 0.440 Chirality : 0.046 0.175 867 Planarity : 0.007 0.097 807 Dihedral : 19.867 103.087 1201 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % 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: -1.24 (0.34), residues: 548 helix: -0.22 (0.30), residues: 270 sheet: -0.52 (0.71), residues: 53 loop : -1.56 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 586 HIS 0.010 0.003 HIS A 606 PHE 0.030 0.003 PHE B 44 TYR 0.023 0.003 TYR B 128 ARG 0.005 0.001 ARG A 484 *********************** 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 93 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 ASP cc_start: 0.6603 (t70) cc_final: 0.6303 (t70) REVERT: B 45 TRP cc_start: 0.8696 (m-10) cc_final: 0.8349 (m-10) REVERT: B 50 ASN cc_start: 0.7839 (t0) cc_final: 0.7540 (t0) REVERT: B 55 ARG cc_start: 0.9034 (ptp-170) cc_final: 0.8599 (ttt180) REVERT: B 401 SER cc_start: 0.9020 (m) cc_final: 0.8614 (p) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1729 time to fit residues: 20.8243 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 : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 1.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5360 Z= 0.325 Angle : 0.754 8.015 7436 Z= 0.386 Chirality : 0.043 0.139 867 Planarity : 0.006 0.086 807 Dihedral : 19.428 96.765 1201 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.22 % Allowed : 2.65 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.02 (0.35), residues: 548 helix: 0.16 (0.32), residues: 270 sheet: -0.93 (0.68), residues: 53 loop : -1.58 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 384 HIS 0.009 0.002 HIS A 606 PHE 0.019 0.002 PHE B 44 TYR 0.020 0.002 TYR A 661 ARG 0.012 0.001 ARG A 488 *********************** 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: 1 poor density : 89 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ASP cc_start: 0.8224 (t0) cc_final: 0.8000 (t0) REVERT: A 470 MET cc_start: 0.8744 (ttm) cc_final: 0.8535 (ttm) REVERT: A 488 ARG cc_start: 0.7739 (ttm110) cc_final: 0.7389 (mtm180) REVERT: A 551 ASN cc_start: 0.8435 (p0) cc_final: 0.8234 (p0) REVERT: A 599 MET cc_start: 0.7037 (ttm) cc_final: 0.6718 (mtp) REVERT: B 50 ASN cc_start: 0.7997 (t0) cc_final: 0.7679 (t0) REVERT: B 128 TYR cc_start: 0.8226 (t80) cc_final: 0.8024 (t80) REVERT: B 145 PHE cc_start: 0.8206 (m-10) cc_final: 0.7769 (m-80) REVERT: B 157 PRO cc_start: 0.8937 (Cg_exo) cc_final: 0.8367 (Cg_endo) REVERT: B 166 LYS cc_start: 0.6759 (mmpt) cc_final: 0.5410 (mmtt) REVERT: B 540 ARG cc_start: 0.7022 (ppt170) cc_final: 0.6562 (ptm160) outliers start: 1 outliers final: 1 residues processed: 89 average time/residue: 0.1768 time to fit residues: 20.2253 Evaluate side-chains 66 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 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 13 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 0.0040 chunk 40 optimal weight: 0.6980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 485 GLN ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 1.1504 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= 0.150 Angle : 0.581 8.576 7436 Z= 0.295 Chirality : 0.038 0.140 867 Planarity : 0.006 0.104 807 Dihedral : 18.804 94.431 1201 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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: -0.37 (0.36), residues: 548 helix: 0.82 (0.33), residues: 269 sheet: -0.65 (0.73), residues: 52 loop : -1.44 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 519 HIS 0.009 0.001 HIS A 489 PHE 0.011 0.001 PHE B 497 TYR 0.013 0.001 TYR A 604 ARG 0.007 0.001 ARG A 488 *********************** 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: 1 poor density : 91 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 LEU cc_start: 0.7985 (tp) cc_final: 0.7612 (tp) REVERT: B 50 ASN cc_start: 0.7628 (t0) cc_final: 0.7218 (t0) REVERT: B 80 MET cc_start: 0.7155 (tpp) cc_final: 0.6566 (tpt) REVERT: B 145 PHE cc_start: 0.7986 (m-10) cc_final: 0.7748 (m-80) REVERT: B 540 ARG cc_start: 0.7065 (ppt170) cc_final: 0.6784 (ptm160) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.1619 time to fit residues: 19.3322 Evaluate side-chains 60 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 0.0170 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.0970 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN ** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 1.1642 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= 0.133 Angle : 0.562 7.278 7436 Z= 0.282 Chirality : 0.038 0.134 867 Planarity : 0.005 0.105 807 Dihedral : 18.504 93.540 1201 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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: -0.03 (0.36), residues: 548 helix: 1.10 (0.33), residues: 270 sheet: 0.10 (0.76), residues: 48 loop : -1.42 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 384 HIS 0.003 0.001 HIS A 606 PHE 0.015 0.001 PHE B 497 TYR 0.012 0.001 TYR A 604 ARG 0.002 0.000 ARG A 484 *********************** 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 77 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LEU cc_start: 0.7970 (tp) cc_final: 0.7587 (tp) REVERT: B 50 ASN cc_start: 0.7373 (t0) cc_final: 0.7048 (t0) REVERT: B 80 MET cc_start: 0.7269 (tpp) cc_final: 0.6831 (tpt) REVERT: B 540 ARG cc_start: 0.7515 (ppt170) cc_final: 0.7207 (ptm160) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1552 time to fit residues: 16.2355 Evaluate side-chains 58 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 1.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5360 Z= 0.159 Angle : 0.566 7.557 7436 Z= 0.282 Chirality : 0.038 0.137 867 Planarity : 0.006 0.097 807 Dihedral : 18.443 93.165 1201 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.37), residues: 548 helix: 1.28 (0.33), residues: 264 sheet: 0.33 (0.80), residues: 49 loop : -1.39 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 384 HIS 0.004 0.001 HIS A 606 PHE 0.031 0.002 PHE A 523 TYR 0.011 0.001 TYR B 391 ARG 0.005 0.000 ARG B 95 *********************** 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 76 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 LEU cc_start: 0.7916 (tp) cc_final: 0.7560 (tp) REVERT: B 50 ASN cc_start: 0.7493 (t0) cc_final: 0.7063 (t0) REVERT: B 80 MET cc_start: 0.7311 (tpp) cc_final: 0.6811 (tpt) REVERT: B 540 ARG cc_start: 0.7473 (ppt170) cc_final: 0.7179 (ptm160) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1351 time to fit residues: 14.6779 Evaluate side-chains 60 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 1.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 5360 Z= 0.377 Angle : 0.780 7.437 7436 Z= 0.398 Chirality : 0.044 0.179 867 Planarity : 0.007 0.096 807 Dihedral : 19.398 96.291 1201 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % 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: -0.79 (0.35), residues: 548 helix: 0.50 (0.32), residues: 268 sheet: -0.68 (0.72), residues: 55 loop : -1.72 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 45 HIS 0.011 0.003 HIS A 606 PHE 0.033 0.003 PHE A 523 TYR 0.014 0.002 TYR B 159 ARG 0.005 0.001 ARG B 95 *********************** 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 78 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 ASP cc_start: 0.6625 (t70) cc_final: 0.6344 (t70) REVERT: B 50 ASN cc_start: 0.7945 (t0) cc_final: 0.7568 (t0) REVERT: B 80 MET cc_start: 0.7574 (tpp) cc_final: 0.7216 (tpt) REVERT: B 166 LYS cc_start: 0.7121 (mmpt) cc_final: 0.6532 (mmmt) REVERT: B 540 ARG cc_start: 0.7679 (ppt170) cc_final: 0.7318 (ptm160) outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1480 time to fit residues: 16.0103 Evaluate side-chains 57 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 0.0070 chunk 28 optimal weight: 9.9990 chunk 36 optimal weight: 0.0060 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 overall best weight: 0.4814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 1.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5360 Z= 0.139 Angle : 0.570 7.328 7436 Z= 0.280 Chirality : 0.038 0.131 867 Planarity : 0.006 0.094 807 Dihedral : 18.698 93.247 1201 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % 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: -0.16 (0.36), residues: 548 helix: 1.05 (0.33), residues: 269 sheet: -0.12 (0.75), residues: 53 loop : -1.53 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 45 HIS 0.003 0.001 HIS A 489 PHE 0.024 0.002 PHE A 523 TYR 0.018 0.001 TYR A 661 ARG 0.003 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 84 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 ASP cc_start: 0.6686 (t70) cc_final: 0.6088 (t70) REVERT: A 593 ASP cc_start: 0.3755 (m-30) cc_final: 0.2706 (t70) REVERT: B 38 ILE cc_start: 0.7692 (mt) cc_final: 0.7187 (mm) REVERT: B 50 ASN cc_start: 0.7553 (t0) cc_final: 0.7129 (t0) REVERT: B 80 MET cc_start: 0.7230 (tpp) cc_final: 0.6433 (tpt) REVERT: B 502 ASP cc_start: 0.6817 (m-30) cc_final: 0.6276 (m-30) REVERT: B 540 ARG cc_start: 0.7451 (ppt170) cc_final: 0.7150 (ptm160) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.1407 time to fit residues: 16.3534 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 : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.150784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.128877 restraints weight = 13245.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.130087 restraints weight = 11624.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.130728 restraints weight = 9448.304| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 1.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5360 Z= 0.172 Angle : 0.600 7.791 7436 Z= 0.294 Chirality : 0.039 0.220 867 Planarity : 0.006 0.091 807 Dihedral : 18.584 93.603 1201 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.22 % Allowed : 0.44 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.37), residues: 548 helix: 1.12 (0.33), residues: 269 sheet: -0.13 (0.74), residues: 55 loop : -1.52 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 45 HIS 0.005 0.001 HIS A 606 PHE 0.009 0.001 PHE B 44 TYR 0.011 0.002 TYR B 532 ARG 0.003 0.000 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1266.44 seconds wall clock time: 23 minutes 43.83 seconds (1423.83 seconds total)