Starting phenix.real_space_refine on Sat Aug 3 01:30:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3z_18878/08_2024/8r3z_18878.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3z_18878/08_2024/8r3z_18878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3z_18878/08_2024/8r3z_18878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3z_18878/08_2024/8r3z_18878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3z_18878/08_2024/8r3z_18878.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3z_18878/08_2024/8r3z_18878.cif" } resolution = 3.4 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 73 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 18 5.16 5 C 4100 2.51 5 N 1107 2.21 5 O 1157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 623": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6389 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 6256 Classifications: {'peptide': 755} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 725} Chain breaks: 5 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 4} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.17, per 1000 atoms: 0.81 Number of scatterers: 6389 At special positions: 0 Unit cell: (71.5, 81.9, 105.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 6 15.00 Mg 1 11.99 O 1157 8.00 N 1107 7.00 C 4100 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 - 3.50 Amino acid : False - 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: 2.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 37.4% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 58 through 72 Processing helix chain 'A' and resid 118 through 133 Processing helix chain 'A' and resid 154 through 165 Processing helix chain 'A' and resid 219 through 230 Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 283 through 291 Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 370 through 380 removed outlier: 3.996A pdb=" N TRP A 380 " --> pdb=" O PHE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 445 through 463 Processing helix chain 'A' and resid 479 through 488 removed outlier: 3.572A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 508 through 522 removed outlier: 3.508A pdb=" N TYR A 512 " --> pdb=" O ASN A 508 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 removed outlier: 3.976A pdb=" N ASP A 537 " --> pdb=" O LYS A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 556 removed outlier: 3.623A pdb=" N CYS A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 644 removed outlier: 3.570A pdb=" N GLN A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 680 Processing helix chain 'A' and resid 680 through 685 removed outlier: 4.646A pdb=" N GLU A 685 " --> pdb=" O SER A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 773 removed outlier: 3.672A pdb=" N PHE A 764 " --> pdb=" O VAL A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 801 removed outlier: 3.634A pdb=" N ALA A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 3.611A pdb=" N LEU A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN A 812 " --> pdb=" O PRO A 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 807 through 812' Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 392 removed outlier: 3.934A pdb=" N ILE A 389 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 31 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A 391 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP A 28 " --> pdb=" O LYS A 706 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 706 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 138 removed outlier: 4.897A pdb=" N LEU A 332 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS A 217 " --> pdb=" O CYS A 330 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS A 330 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ARG A 244 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 168 through 170 removed outlier: 3.547A pdb=" N ASN A 203 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.657A pdb=" N ILE A 43 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR A 112 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE A 45 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA6, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA7, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.583A pdb=" N THR A 719 " --> pdb=" O VAL A 736 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 731 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A 749 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 692 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN A 755 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE A 690 " --> pdb=" O ASN A 755 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 602 " --> pdb=" O THR A 611 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 407 through 409 removed outlier: 3.538A pdb=" N ILE A 401 " --> pdb=" O PHE A 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 475 removed outlier: 6.116A pdb=" N ILE A 437 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL A 475 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR A 439 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 528 " --> pdb=" O ILE A 500 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2008 1.34 - 1.46: 1241 1.46 - 1.58: 3251 1.58 - 1.70: 12 1.70 - 1.82: 29 Bond restraints: 6541 Sorted by residual: bond pdb=" N LEU A 774 " pdb=" CA LEU A 774 " ideal model delta sigma weight residual 1.458 1.488 -0.030 9.00e-03 1.23e+04 1.12e+01 bond pdb=" N ILE A 770 " pdb=" CA ILE A 770 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.98e+00 bond pdb=" N ASN A 700 " pdb=" CA ASN A 700 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.69e+00 bond pdb=" N ASN A 203 " pdb=" CA ASN A 203 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 6.05e+00 bond pdb=" N LEU A 771 " pdb=" CA LEU A 771 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.52e+00 ... (remaining 6536 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.81: 141 105.81 - 112.87: 3522 112.87 - 119.93: 2166 119.93 - 126.99: 2950 126.99 - 134.06: 83 Bond angle restraints: 8862 Sorted by residual: angle pdb=" N ASN A 756 " pdb=" CA ASN A 756 " pdb=" C ASN A 756 " ideal model delta sigma weight residual 114.56 107.72 6.84 1.27e+00 6.20e-01 2.90e+01 angle pdb=" CA PRO A 489 " pdb=" N PRO A 489 " pdb=" CD PRO A 489 " ideal model delta sigma weight residual 112.00 105.82 6.18 1.40e+00 5.10e-01 1.95e+01 angle pdb=" CA ASN A 756 " pdb=" C ASN A 756 " pdb=" N THR A 757 " ideal model delta sigma weight residual 119.26 115.57 3.69 1.14e+00 7.69e-01 1.05e+01 angle pdb=" N ASN A 700 " pdb=" CA ASN A 700 " pdb=" C ASN A 700 " ideal model delta sigma weight residual 112.59 108.92 3.67 1.22e+00 6.72e-01 9.06e+00 angle pdb=" CB MET A 224 " pdb=" CG MET A 224 " pdb=" SD MET A 224 " ideal model delta sigma weight residual 112.70 121.53 -8.83 3.00e+00 1.11e-01 8.67e+00 ... (remaining 8857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 3348 17.46 - 34.91: 457 34.91 - 52.37: 117 52.37 - 69.83: 38 69.83 - 87.28: 7 Dihedral angle restraints: 3967 sinusoidal: 1731 harmonic: 2236 Sorted by residual: dihedral pdb=" CA SER A 390 " pdb=" C SER A 390 " pdb=" N MET A 391 " pdb=" CA MET A 391 " ideal model delta harmonic sigma weight residual -180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA GLU A 30 " pdb=" C GLU A 30 " pdb=" N MET A 31 " pdb=" CA MET A 31 " ideal model delta harmonic sigma weight residual -180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LEU A 181 " pdb=" C LEU A 181 " pdb=" N THR A 182 " pdb=" CA THR A 182 " ideal model delta harmonic sigma weight residual 180.00 164.19 15.81 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 3964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 766 0.051 - 0.101: 175 0.101 - 0.152: 41 0.152 - 0.203: 3 0.203 - 0.253: 1 Chirality restraints: 986 Sorted by residual: chirality pdb=" CB ILE A 500 " pdb=" CA ILE A 500 " pdb=" CG1 ILE A 500 " pdb=" CG2 ILE A 500 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ILE A 770 " pdb=" N ILE A 770 " pdb=" C ILE A 770 " pdb=" CB ILE A 770 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CA LEU A 771 " pdb=" N LEU A 771 " pdb=" C LEU A 771 " pdb=" CB LEU A 771 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 983 not shown) Planarity restraints: 1098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 488 " -0.083 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO A 489 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO A 489 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 489 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 568 " 0.014 2.00e-02 2.50e+03 1.43e-02 5.11e+00 pdb=" CG TRP A 568 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 568 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 568 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 568 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 568 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 568 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 568 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 568 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 568 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 121 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C LEU A 121 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU A 121 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A 122 " 0.012 2.00e-02 2.50e+03 ... (remaining 1095 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 52 2.53 - 3.12: 4732 3.12 - 3.71: 10155 3.71 - 4.31: 13771 4.31 - 4.90: 23114 Nonbonded interactions: 51824 Sorted by model distance: nonbonded pdb=" OP3 U B 1 " pdb="MG MG A1000 " model vdw 1.932 2.170 nonbonded pdb=" O LYS A 697 " pdb=" NH2 ARG A 783 " model vdw 2.241 3.120 nonbonded pdb=" NE2 GLN A 354 " pdb=" O PHE A 742 " model vdw 2.255 3.120 nonbonded pdb=" NZ LYS A 86 " pdb=" O VAL A 379 " model vdw 2.256 3.120 nonbonded pdb=" OG1 THR A 157 " pdb=" OD2 ASP A 372 " model vdw 2.259 3.040 ... (remaining 51819 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 individual isotropic 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 23.160 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 0.004 0.091 6541 Z= 0.216 Angle : 0.653 8.835 8862 Z= 0.367 Chirality : 0.046 0.253 986 Planarity : 0.005 0.123 1098 Dihedral : 17.436 87.284 2517 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.29 % Allowed : 27.82 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.30), residues: 743 helix: 0.92 (0.33), residues: 252 sheet: -0.36 (0.35), residues: 193 loop : -0.80 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 568 HIS 0.008 0.001 HIS A 687 PHE 0.011 0.001 PHE A 481 TYR 0.032 0.002 TYR A 57 ARG 0.002 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8747 (mmmt) REVERT: A 416 ASN cc_start: 0.8505 (p0) cc_final: 0.7929 (p0) REVERT: A 417 TRP cc_start: 0.6963 (m100) cc_final: 0.6463 (m100) outliers start: 2 outliers final: 0 residues processed: 85 average time/residue: 0.1657 time to fit residues: 19.4324 Evaluate side-chains 67 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 0.0570 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 GLN A 551 GLN A 707 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6541 Z= 0.212 Angle : 0.540 7.131 8862 Z= 0.285 Chirality : 0.044 0.174 986 Planarity : 0.004 0.067 1098 Dihedral : 9.372 63.836 916 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.14 % Allowed : 25.53 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.30), residues: 743 helix: 1.21 (0.33), residues: 250 sheet: -0.16 (0.36), residues: 187 loop : -0.76 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 568 HIS 0.006 0.001 HIS A 687 PHE 0.013 0.001 PHE A 408 TYR 0.015 0.001 TYR A 816 ARG 0.002 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 75 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.9202 (mmtt) cc_final: 0.8959 (pttm) REVERT: A 84 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: A 85 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8115 (mp10) REVERT: A 224 MET cc_start: 0.9147 (mmm) cc_final: 0.8567 (mmm) REVERT: A 391 MET cc_start: 0.6699 (ttt) cc_final: 0.6392 (ttt) REVERT: A 417 TRP cc_start: 0.6847 (m100) cc_final: 0.6326 (m100) REVERT: A 438 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6232 (tp) REVERT: A 531 VAL cc_start: 0.7147 (OUTLIER) cc_final: 0.6945 (m) outliers start: 29 outliers final: 14 residues processed: 100 average time/residue: 0.1643 time to fit residues: 22.6530 Evaluate side-chains 85 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 774 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A 551 GLN A 777 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6541 Z= 0.273 Angle : 0.561 7.103 8862 Z= 0.292 Chirality : 0.044 0.140 986 Planarity : 0.004 0.045 1098 Dihedral : 9.387 63.840 916 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.56 % Allowed : 25.39 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.30), residues: 743 helix: 1.17 (0.32), residues: 252 sheet: -0.16 (0.36), residues: 185 loop : -0.72 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 568 HIS 0.009 0.001 HIS A 687 PHE 0.026 0.001 PHE A 408 TYR 0.014 0.001 TYR A 816 ARG 0.007 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 65 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.9215 (mmtt) cc_final: 0.8788 (mmmt) REVERT: A 84 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: A 224 MET cc_start: 0.9210 (mmm) cc_final: 0.8771 (mmm) REVERT: A 355 MET cc_start: 0.7950 (mpp) cc_final: 0.7374 (mpp) REVERT: A 416 ASN cc_start: 0.8594 (p0) cc_final: 0.7978 (p0) REVERT: A 417 TRP cc_start: 0.6852 (m100) cc_final: 0.6510 (m100) REVERT: A 498 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: A 531 VAL cc_start: 0.7238 (OUTLIER) cc_final: 0.7017 (m) outliers start: 39 outliers final: 26 residues processed: 98 average time/residue: 0.1592 time to fit residues: 21.9336 Evaluate side-chains 89 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 60 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 588 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 794 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6541 Z= 0.193 Angle : 0.511 6.577 8862 Z= 0.266 Chirality : 0.043 0.141 986 Planarity : 0.003 0.034 1098 Dihedral : 9.285 63.836 916 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.56 % Allowed : 26.96 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.30), residues: 743 helix: 1.40 (0.33), residues: 248 sheet: -0.12 (0.37), residues: 185 loop : -0.66 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 417 HIS 0.006 0.001 HIS A 687 PHE 0.019 0.001 PHE A 408 TYR 0.011 0.001 TYR A 816 ARG 0.003 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 69 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8013 (mp) REVERT: A 82 LYS cc_start: 0.9228 (mmtt) cc_final: 0.8777 (mmmt) REVERT: A 85 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8067 (mp10) REVERT: A 224 MET cc_start: 0.9203 (mmm) cc_final: 0.8793 (mmm) REVERT: A 352 ASN cc_start: 0.8735 (m-40) cc_final: 0.8252 (m110) REVERT: A 355 MET cc_start: 0.7983 (mpp) cc_final: 0.7437 (mpp) REVERT: A 416 ASN cc_start: 0.8549 (p0) cc_final: 0.7754 (t0) REVERT: A 498 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7622 (pm20) REVERT: A 531 VAL cc_start: 0.7160 (OUTLIER) cc_final: 0.6914 (m) REVERT: A 533 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8901 (tmtt) outliers start: 32 outliers final: 19 residues processed: 95 average time/residue: 0.1496 time to fit residues: 20.3896 Evaluate side-chains 90 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 66 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 588 HIS Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 774 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 777 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6541 Z= 0.409 Angle : 0.633 8.852 8862 Z= 0.328 Chirality : 0.045 0.152 986 Planarity : 0.004 0.036 1098 Dihedral : 9.422 64.115 916 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.70 % Allowed : 25.11 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.30), residues: 743 helix: 1.02 (0.32), residues: 252 sheet: -0.30 (0.38), residues: 179 loop : -0.72 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 417 HIS 0.011 0.001 HIS A 687 PHE 0.022 0.002 PHE A 408 TYR 0.019 0.002 TYR A 46 ARG 0.003 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 69 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7949 (mp) REVERT: A 333 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8074 (t80) REVERT: A 355 MET cc_start: 0.8029 (mpp) cc_final: 0.7464 (mpp) REVERT: A 531 VAL cc_start: 0.7419 (OUTLIER) cc_final: 0.7085 (m) REVERT: A 533 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8975 (tmtt) REVERT: A 776 TYR cc_start: 0.8576 (m-10) cc_final: 0.8141 (m-80) outliers start: 47 outliers final: 33 residues processed: 109 average time/residue: 0.1574 time to fit residues: 23.8898 Evaluate side-chains 102 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 65 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 588 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 794 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN A 645 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6541 Z= 0.201 Angle : 0.542 7.446 8862 Z= 0.279 Chirality : 0.044 0.172 986 Planarity : 0.003 0.036 1098 Dihedral : 9.290 63.920 916 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.99 % Allowed : 26.53 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.30), residues: 743 helix: 1.30 (0.33), residues: 248 sheet: -0.36 (0.37), residues: 184 loop : -0.65 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 568 HIS 0.008 0.001 HIS A 687 PHE 0.014 0.001 PHE A 408 TYR 0.011 0.001 TYR A 46 ARG 0.008 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 68 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8035 (mp) REVERT: A 224 MET cc_start: 0.9160 (mmm) cc_final: 0.8578 (mmm) REVERT: A 391 MET cc_start: 0.6813 (ttt) cc_final: 0.6611 (ttt) REVERT: A 416 ASN cc_start: 0.8496 (p0) cc_final: 0.7862 (t0) REVERT: A 531 VAL cc_start: 0.7307 (OUTLIER) cc_final: 0.7085 (m) REVERT: A 533 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.8920 (tmtt) outliers start: 35 outliers final: 22 residues processed: 100 average time/residue: 0.1565 time to fit residues: 22.1004 Evaluate side-chains 88 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 588 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 774 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6541 Z= 0.228 Angle : 0.549 7.689 8862 Z= 0.281 Chirality : 0.044 0.169 986 Planarity : 0.003 0.041 1098 Dihedral : 9.204 63.984 916 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.14 % Allowed : 26.53 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.30), residues: 743 helix: 1.35 (0.33), residues: 248 sheet: -0.26 (0.37), residues: 179 loop : -0.71 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 417 HIS 0.006 0.001 HIS A 687 PHE 0.014 0.001 PHE A 408 TYR 0.012 0.001 TYR A 46 ARG 0.011 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 64 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8016 (mp) REVERT: A 82 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8929 (mmmt) REVERT: A 224 MET cc_start: 0.9172 (mmm) cc_final: 0.8647 (mmm) REVERT: A 416 ASN cc_start: 0.8547 (p0) cc_final: 0.7665 (t0) REVERT: A 431 GLU cc_start: 0.8978 (mp0) cc_final: 0.8713 (mp0) REVERT: A 531 VAL cc_start: 0.7299 (OUTLIER) cc_final: 0.7072 (m) REVERT: A 533 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8935 (tmtt) REVERT: A 776 TYR cc_start: 0.8531 (m-10) cc_final: 0.8111 (m-80) outliers start: 36 outliers final: 27 residues processed: 96 average time/residue: 0.1554 time to fit residues: 21.3385 Evaluate side-chains 88 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 58 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 588 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 774 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6541 Z= 0.176 Angle : 0.541 7.895 8862 Z= 0.275 Chirality : 0.044 0.175 986 Planarity : 0.003 0.047 1098 Dihedral : 9.144 63.890 916 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.57 % Allowed : 28.10 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.30), residues: 743 helix: 1.49 (0.33), residues: 248 sheet: -0.12 (0.37), residues: 185 loop : -0.70 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 568 HIS 0.006 0.001 HIS A 687 PHE 0.011 0.001 PHE A 408 TYR 0.011 0.001 TYR A 46 ARG 0.012 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 65 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8014 (mp) REVERT: A 82 LYS cc_start: 0.9215 (mmmt) cc_final: 0.8933 (mmmt) REVERT: A 224 MET cc_start: 0.9176 (mmm) cc_final: 0.8675 (mmm) REVERT: A 416 ASN cc_start: 0.8470 (p0) cc_final: 0.7878 (t0) REVERT: A 431 GLU cc_start: 0.8961 (mp0) cc_final: 0.8695 (mp0) REVERT: A 533 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8919 (tmtt) outliers start: 25 outliers final: 19 residues processed: 87 average time/residue: 0.1544 time to fit residues: 19.1772 Evaluate side-chains 78 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 57 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 588 HIS Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 765 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 43 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6541 Z= 0.159 Angle : 0.525 7.727 8862 Z= 0.269 Chirality : 0.044 0.180 986 Planarity : 0.003 0.053 1098 Dihedral : 9.071 63.875 916 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.71 % Allowed : 29.24 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.30), residues: 743 helix: 1.60 (0.33), residues: 248 sheet: 0.03 (0.37), residues: 184 loop : -0.70 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 417 HIS 0.005 0.001 HIS A 687 PHE 0.011 0.001 PHE A 408 TYR 0.012 0.001 TYR A 249 ARG 0.013 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8012 (mp) REVERT: A 82 LYS cc_start: 0.9208 (mmmt) cc_final: 0.8931 (mmmt) REVERT: A 224 MET cc_start: 0.9170 (mmm) cc_final: 0.8723 (mmm) REVERT: A 416 ASN cc_start: 0.8603 (p0) cc_final: 0.7434 (t0) REVERT: A 533 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8916 (tmtt) outliers start: 19 outliers final: 17 residues processed: 81 average time/residue: 0.1551 time to fit residues: 18.0941 Evaluate side-chains 75 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 56 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 765 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6541 Z= 0.229 Angle : 0.553 8.077 8862 Z= 0.283 Chirality : 0.044 0.176 986 Planarity : 0.003 0.049 1098 Dihedral : 9.100 63.959 916 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.14 % Allowed : 28.82 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.30), residues: 743 helix: 1.57 (0.33), residues: 248 sheet: -0.01 (0.37), residues: 178 loop : -0.77 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP A 417 HIS 0.008 0.001 HIS A 687 PHE 0.012 0.001 PHE A 408 TYR 0.013 0.001 TYR A 249 ARG 0.012 0.000 ARG A 619 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7921 (mp) REVERT: A 82 LYS cc_start: 0.9224 (mmmt) cc_final: 0.8946 (mmmt) REVERT: A 416 ASN cc_start: 0.8423 (p0) cc_final: 0.7830 (t0) REVERT: A 431 GLU cc_start: 0.8964 (mp0) cc_final: 0.8710 (mp0) REVERT: A 533 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8924 (tmtt) outliers start: 22 outliers final: 20 residues processed: 81 average time/residue: 0.1539 time to fit residues: 17.7921 Evaluate side-chains 80 residues out of total 701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 679 ASN Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 765 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.6980 chunk 8 optimal weight: 0.0970 chunk 16 optimal weight: 0.0870 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.127858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.098180 restraints weight = 15602.267| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 4.91 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6541 Z= 0.140 Angle : 0.526 9.332 8862 Z= 0.265 Chirality : 0.044 0.187 986 Planarity : 0.003 0.049 1098 Dihedral : 9.046 63.829 916 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.57 % Allowed : 29.53 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.30), residues: 743 helix: 1.70 (0.33), residues: 251 sheet: 0.10 (0.39), residues: 163 loop : -0.63 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 417 HIS 0.003 0.001 HIS A 109 PHE 0.009 0.001 PHE A 408 TYR 0.011 0.001 TYR A 249 ARG 0.012 0.000 ARG A 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1689.94 seconds wall clock time: 30 minutes 56.74 seconds (1856.74 seconds total)