Starting phenix.real_space_refine on Mon Apr 28 02:22:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijy_60645/04_2025/9ijy_60645_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijy_60645/04_2025/9ijy_60645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ijy_60645/04_2025/9ijy_60645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijy_60645/04_2025/9ijy_60645.map" model { file = "/net/cci-nas-00/data/ceres_data/9ijy_60645/04_2025/9ijy_60645_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijy_60645/04_2025/9ijy_60645_trim.cif" } resolution = 2.64 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= 0.057 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 4 5.49 5 S 32 5.16 5 C 4474 2.51 5 N 1054 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6654 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3270 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 13, 'TRANS': 378} Chain breaks: 1 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'6PL': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 6.21, per 1000 atoms: 0.93 Number of scatterers: 6654 At special positions: 0 Unit cell: (71.764, 123.956, 78.288, 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 32 16.00 P 4 15.00 O 1090 8.00 N 1054 7.00 C 4474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.03 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: 1.80 Conformation dependent library (CDL) restraints added in 833.2 milliseconds 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 76.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 230 through 257 Processing helix chain 'A' and resid 265 through 294 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 336 Processing helix chain 'A' and resid 345 through 361 removed outlier: 3.923A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 390 through 403 Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.807A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.594A pdb=" N HIS A 441 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 442 " --> pdb=" O ILE A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 442' Processing helix chain 'A' and resid 446 through 470 removed outlier: 3.873A pdb=" N ILE A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 475 through 503 removed outlier: 4.170A pdb=" N GLU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 532 removed outlier: 4.536A pdb=" N VAL A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 582 removed outlier: 4.012A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 618 Proline residue: A 598 - end of helix removed outlier: 3.823A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 257 Processing helix chain 'B' and resid 265 through 294 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 312 through 336 Processing helix chain 'B' and resid 345 through 361 removed outlier: 3.923A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 403 through 419 removed outlier: 3.807A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 442 removed outlier: 3.594A pdb=" N HIS B 441 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 442 " --> pdb=" O ILE B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 442' Processing helix chain 'B' and resid 446 through 470 removed outlier: 3.873A pdb=" N ILE B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 475 through 503 removed outlier: 4.170A pdb=" N GLU B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 532 removed outlier: 4.536A pdb=" N VAL B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 582 removed outlier: 4.012A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 618 Proline residue: B 598 - end of helix removed outlier: 3.823A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1368 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: 1.78 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 950 1.31 - 1.43: 2110 1.43 - 1.56: 3758 1.56 - 1.68: 4 1.68 - 1.81: 44 Bond restraints: 6866 Sorted by residual: bond pdb=" CA ARG A 603 " pdb=" C ARG A 603 " ideal model delta sigma weight residual 1.523 1.446 0.077 1.30e-02 5.92e+03 3.54e+01 bond pdb=" CA ARG B 603 " pdb=" C ARG B 603 " ideal model delta sigma weight residual 1.523 1.446 0.077 1.30e-02 5.92e+03 3.54e+01 bond pdb=" C11 6PL B1002 " pdb=" O3 6PL B1002 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C11 6PL A1002 " pdb=" O3 6PL A1002 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C ARG A 603 " pdb=" O ARG A 603 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.17e-02 7.31e+03 2.40e+01 ... (remaining 6861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 9244 3.79 - 7.57: 64 7.57 - 11.36: 6 11.36 - 15.14: 0 15.14 - 18.93: 4 Bond angle restraints: 9318 Sorted by residual: angle pdb=" O1P 6PL A1002 " pdb=" P 6PL A1002 " pdb=" O2P 6PL A1002 " ideal model delta sigma weight residual 119.71 100.78 18.93 3.00e+00 1.11e-01 3.98e+01 angle pdb=" O1P 6PL B1002 " pdb=" P 6PL B1002 " pdb=" O2P 6PL B1002 " ideal model delta sigma weight residual 119.71 100.78 18.93 3.00e+00 1.11e-01 3.98e+01 angle pdb=" O3P 6PL A1002 " pdb=" P 6PL A1002 " pdb=" O4P 6PL A1002 " ideal model delta sigma weight residual 93.65 110.81 -17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" O3P 6PL B1002 " pdb=" P 6PL B1002 " pdb=" O4P 6PL B1002 " ideal model delta sigma weight residual 93.65 110.81 -17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" O PHE A 602 " pdb=" C PHE A 602 " pdb=" N ARG A 603 " ideal model delta sigma weight residual 122.15 118.12 4.03 1.14e+00 7.69e-01 1.25e+01 ... (remaining 9313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 3316 16.33 - 32.65: 428 32.65 - 48.98: 134 48.98 - 65.30: 34 65.30 - 81.63: 8 Dihedral angle restraints: 3920 sinusoidal: 1610 harmonic: 2310 Sorted by residual: dihedral pdb=" CA PRO A 475 " pdb=" C PRO A 475 " pdb=" N HIS A 476 " pdb=" CA HIS A 476 " ideal model delta harmonic sigma weight residual -180.00 -162.98 -17.02 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA PRO B 475 " pdb=" C PRO B 475 " pdb=" N HIS B 476 " pdb=" CA HIS B 476 " ideal model delta harmonic sigma weight residual -180.00 -162.98 -17.02 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CG ARG B 468 " pdb=" CD ARG B 468 " pdb=" NE ARG B 468 " pdb=" CZ ARG B 468 " ideal model delta sinusoidal sigma weight residual 90.00 132.85 -42.85 2 1.50e+01 4.44e-03 9.87e+00 ... (remaining 3917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 792 0.049 - 0.098: 192 0.098 - 0.147: 14 0.147 - 0.196: 6 0.196 - 0.245: 2 Chirality restraints: 1006 Sorted by residual: chirality pdb=" CA ARG B 603 " pdb=" N ARG B 603 " pdb=" C ARG B 603 " pdb=" CB ARG B 603 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ARG A 603 " pdb=" N ARG A 603 " pdb=" C ARG A 603 " pdb=" CB ARG A 603 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C2 6PL B1002 " pdb=" C1 6PL B1002 " pdb=" C3 6PL B1002 " pdb=" O2 6PL B1002 " both_signs ideal model delta sigma weight residual False -2.33 -2.51 0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 1003 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 549 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" CD GLU B 549 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU B 549 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU B 549 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 549 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" CD GLU A 549 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU A 549 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU A 549 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 475 " -0.005 2.00e-02 2.50e+03 1.04e-02 1.08e+00 pdb=" C PRO B 475 " 0.018 2.00e-02 2.50e+03 pdb=" O PRO B 475 " -0.007 2.00e-02 2.50e+03 pdb=" N HIS B 476 " -0.006 2.00e-02 2.50e+03 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 914 2.75 - 3.29: 6860 3.29 - 3.83: 11788 3.83 - 4.36: 13723 4.36 - 4.90: 23451 Nonbonded interactions: 56736 Sorted by model distance: nonbonded pdb=" O ILE A 271 " pdb=" OH TYR A 352 " model vdw 2.215 3.040 nonbonded pdb=" O ILE B 271 " pdb=" OH TYR B 352 " model vdw 2.215 3.040 nonbonded pdb=" O ASN B 618 " pdb=" OD1 ASN B 618 " model vdw 2.245 3.040 nonbonded pdb=" O ASN A 618 " pdb=" OD1 ASN A 618 " model vdw 2.245 3.040 nonbonded pdb=" O TRP B 534 " pdb=" NH1 ARG B 548 " model vdw 2.254 3.120 ... (remaining 56731 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.450 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.100 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 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 : 0.005 0.103 6868 Z= 0.292 Angle : 0.837 18.927 9322 Z= 0.411 Chirality : 0.042 0.245 1006 Planarity : 0.004 0.032 1122 Dihedral : 16.724 81.626 2426 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.29 % Allowed : 24.21 % Favored : 75.50 % 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 (0.29), residues: 776 helix: 0.93 (0.20), residues: 564 sheet: None (None), residues: 0 loop : -2.41 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 514 HIS 0.003 0.001 HIS B 476 PHE 0.012 0.001 PHE A 610 TYR 0.008 0.001 TYR A 512 ARG 0.006 0.001 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.11180 ( 456) hydrogen bonds : angle 5.34194 ( 1368) SS BOND : bond 0.00094 ( 2) SS BOND : angle 0.08432 ( 4) covalent geometry : bond 0.00545 ( 6866) covalent geometry : angle 0.83710 ( 9318) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.705 Fit side-chains REVERT: A 532 MET cc_start: 0.8617 (mmm) cc_final: 0.8342 (mmp) REVERT: A 592 ILE cc_start: 0.8170 (pt) cc_final: 0.7675 (pt) REVERT: B 532 MET cc_start: 0.8617 (mmm) cc_final: 0.8342 (mmp) REVERT: B 592 ILE cc_start: 0.8168 (pt) cc_final: 0.7673 (pt) outliers start: 2 outliers final: 2 residues processed: 126 average time/residue: 1.0513 time to fit residues: 140.3974 Evaluate side-chains 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 570 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 6.9990 chunk 59 optimal weight: 0.0470 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 61 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 70 optimal weight: 0.0980 overall best weight: 0.2078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 618 ASN B 294 GLN B 618 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.179233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136947 restraints weight = 7705.482| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.24 r_work: 0.3473 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6868 Z= 0.133 Angle : 0.573 7.694 9322 Z= 0.298 Chirality : 0.040 0.140 1006 Planarity : 0.004 0.052 1122 Dihedral : 10.679 74.309 968 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.90 % Allowed : 19.88 % Favored : 75.22 % 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: 1.06 (0.29), residues: 776 helix: 1.69 (0.20), residues: 558 sheet: None (None), residues: 0 loop : -2.00 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 514 HIS 0.002 0.001 HIS B 441 PHE 0.019 0.001 PHE B 391 TYR 0.012 0.001 TYR B 352 ARG 0.004 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.05175 ( 456) hydrogen bonds : angle 4.45003 ( 1368) SS BOND : bond 0.00003 ( 2) SS BOND : angle 0.03685 ( 4) covalent geometry : bond 0.00270 ( 6866) covalent geometry : angle 0.57322 ( 9318) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.777 Fit side-chains REVERT: A 294 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.5915 (mp-120) REVERT: A 366 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.4503 (t80) REVERT: A 369 LYS cc_start: 0.7346 (pmtt) cc_final: 0.6992 (ptpp) REVERT: A 448 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6491 (ptp90) REVERT: A 500 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8195 (mmmm) REVERT: A 592 ILE cc_start: 0.8169 (pt) cc_final: 0.7700 (pt) REVERT: B 294 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.5922 (mp-120) REVERT: B 366 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.4500 (t80) REVERT: B 369 LYS cc_start: 0.7341 (pmtt) cc_final: 0.6987 (ptpp) REVERT: B 448 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.6489 (ptp90) REVERT: B 500 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8195 (mmmm) REVERT: B 592 ILE cc_start: 0.8162 (pt) cc_final: 0.7692 (pt) outliers start: 34 outliers final: 10 residues processed: 140 average time/residue: 0.9522 time to fit residues: 141.9392 Evaluate side-chains 126 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 448 ARG Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 540 ASN A 608 ASN A 618 ASN B 294 GLN B 540 ASN B 608 ASN B 618 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.175218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132236 restraints weight = 7801.248| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.27 r_work: 0.3409 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6868 Z= 0.159 Angle : 0.590 7.397 9322 Z= 0.308 Chirality : 0.041 0.133 1006 Planarity : 0.004 0.041 1122 Dihedral : 10.516 70.187 968 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.05 % Allowed : 19.88 % Favored : 74.06 % 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: 1.13 (0.29), residues: 776 helix: 1.75 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -2.22 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 514 HIS 0.003 0.001 HIS B 616 PHE 0.020 0.002 PHE A 391 TYR 0.010 0.002 TYR B 352 ARG 0.004 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.05168 ( 456) hydrogen bonds : angle 4.36863 ( 1368) SS BOND : bond 0.00024 ( 2) SS BOND : angle 0.06822 ( 4) covalent geometry : bond 0.00348 ( 6866) covalent geometry : angle 0.59062 ( 9318) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 0.742 Fit side-chains REVERT: A 253 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8616 (mm) REVERT: A 304 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7253 (mt-10) REVERT: A 366 PHE cc_start: 0.6863 (OUTLIER) cc_final: 0.4538 (t80) REVERT: A 369 LYS cc_start: 0.7309 (pmtt) cc_final: 0.6879 (ptpp) REVERT: A 550 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: A 584 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7350 (mt) REVERT: A 592 ILE cc_start: 0.8129 (pt) cc_final: 0.7708 (pt) REVERT: A 622 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7588 (mm-30) REVERT: B 253 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8626 (mm) REVERT: B 366 PHE cc_start: 0.6862 (OUTLIER) cc_final: 0.4533 (t80) REVERT: B 369 LYS cc_start: 0.7320 (pmtt) cc_final: 0.6886 (ptpp) REVERT: B 550 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: B 584 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7349 (mt) REVERT: B 592 ILE cc_start: 0.8127 (pt) cc_final: 0.7706 (pt) REVERT: B 622 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7584 (mm-30) outliers start: 42 outliers final: 12 residues processed: 136 average time/residue: 1.0310 time to fit residues: 148.5981 Evaluate side-chains 124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 540 ASN A 608 ASN B 294 GLN B 540 ASN B 608 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.172842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.129390 restraints weight = 7773.285| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.27 r_work: 0.3372 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6868 Z= 0.173 Angle : 0.604 7.265 9322 Z= 0.316 Chirality : 0.041 0.131 1006 Planarity : 0.004 0.038 1122 Dihedral : 10.378 67.562 968 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.34 % Allowed : 18.73 % Favored : 74.93 % 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: 1.18 (0.29), residues: 776 helix: 1.77 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -2.13 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 514 HIS 0.003 0.001 HIS B 441 PHE 0.019 0.002 PHE A 391 TYR 0.010 0.002 TYR B 290 ARG 0.004 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.05224 ( 456) hydrogen bonds : angle 4.37676 ( 1368) SS BOND : bond 0.00022 ( 2) SS BOND : angle 0.05036 ( 4) covalent geometry : bond 0.00391 ( 6866) covalent geometry : angle 0.60448 ( 9318) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.795 Fit side-chains REVERT: A 366 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.4494 (t80) REVERT: A 369 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7026 (pttm) REVERT: A 550 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7276 (mt-10) REVERT: A 584 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7365 (mt) REVERT: A 592 ILE cc_start: 0.8234 (pt) cc_final: 0.7853 (pt) REVERT: A 622 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7664 (mm-30) REVERT: A 623 PHE cc_start: 0.6569 (m-80) cc_final: 0.6252 (m-10) REVERT: B 366 PHE cc_start: 0.6784 (OUTLIER) cc_final: 0.4489 (t80) REVERT: B 369 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7023 (pttm) REVERT: B 550 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: B 584 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7360 (mt) REVERT: B 592 ILE cc_start: 0.8236 (pt) cc_final: 0.7855 (pt) REVERT: B 622 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: B 623 PHE cc_start: 0.6578 (m-80) cc_final: 0.6254 (m-10) outliers start: 44 outliers final: 14 residues processed: 132 average time/residue: 1.1824 time to fit residues: 164.8931 Evaluate side-chains 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 540 ASN A 618 ASN B 294 GLN B 540 ASN B 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.173071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129689 restraints weight = 7773.022| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.27 r_work: 0.3376 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6868 Z= 0.156 Angle : 0.587 7.558 9322 Z= 0.307 Chirality : 0.041 0.133 1006 Planarity : 0.004 0.037 1122 Dihedral : 9.996 63.834 968 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.62 % Allowed : 19.31 % Favored : 75.07 % 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: 1.26 (0.29), residues: 776 helix: 1.81 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -2.07 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 514 HIS 0.003 0.001 HIS B 616 PHE 0.017 0.002 PHE A 391 TYR 0.012 0.001 TYR A 352 ARG 0.003 0.000 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.05066 ( 456) hydrogen bonds : angle 4.33028 ( 1368) SS BOND : bond 0.00023 ( 2) SS BOND : angle 0.10364 ( 4) covalent geometry : bond 0.00346 ( 6866) covalent geometry : angle 0.58717 ( 9318) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.831 Fit side-chains REVERT: A 366 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.4606 (t80) REVERT: A 592 ILE cc_start: 0.8197 (pt) cc_final: 0.7862 (pt) REVERT: A 622 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7664 (mm-30) REVERT: A 623 PHE cc_start: 0.6518 (m-80) cc_final: 0.6243 (m-10) REVERT: B 366 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.4601 (t80) REVERT: B 550 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: B 592 ILE cc_start: 0.8202 (pt) cc_final: 0.7867 (pt) REVERT: B 622 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7662 (mm-30) REVERT: B 623 PHE cc_start: 0.6524 (m-80) cc_final: 0.6248 (m-10) outliers start: 39 outliers final: 14 residues processed: 138 average time/residue: 1.1434 time to fit residues: 167.3455 Evaluate side-chains 129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.0470 chunk 77 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 540 ASN A 618 ASN B 294 GLN B 540 ASN B 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.173918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.130474 restraints weight = 7660.091| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.27 r_work: 0.3385 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6868 Z= 0.147 Angle : 0.588 7.888 9322 Z= 0.307 Chirality : 0.041 0.133 1006 Planarity : 0.004 0.032 1122 Dihedral : 9.763 60.390 968 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.47 % Allowed : 20.32 % Favored : 75.22 % 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: 1.32 (0.29), residues: 776 helix: 1.84 (0.20), residues: 572 sheet: None (None), residues: 0 loop : -2.02 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 514 HIS 0.003 0.001 HIS A 616 PHE 0.013 0.002 PHE A 610 TYR 0.012 0.002 TYR A 496 ARG 0.003 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.04930 ( 456) hydrogen bonds : angle 4.31743 ( 1368) SS BOND : bond 0.00028 ( 2) SS BOND : angle 0.05153 ( 4) covalent geometry : bond 0.00323 ( 6866) covalent geometry : angle 0.58805 ( 9318) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.826 Fit side-chains REVERT: A 366 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.4498 (t80) REVERT: A 550 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: A 592 ILE cc_start: 0.8214 (pt) cc_final: 0.7904 (pt) REVERT: A 622 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7417 (mm-30) REVERT: A 623 PHE cc_start: 0.6600 (m-80) cc_final: 0.6275 (m-10) REVERT: B 366 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.4494 (t80) REVERT: B 592 ILE cc_start: 0.8215 (pt) cc_final: 0.7905 (pt) REVERT: B 622 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7423 (mm-30) REVERT: B 623 PHE cc_start: 0.6613 (m-80) cc_final: 0.6286 (m-10) outliers start: 31 outliers final: 12 residues processed: 124 average time/residue: 1.6129 time to fit residues: 211.7513 Evaluate side-chains 127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.0170 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 608 ASN A 618 ASN B 294 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 608 ASN B 618 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.174118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130892 restraints weight = 7741.322| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.26 r_work: 0.3393 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6868 Z= 0.143 Angle : 0.608 9.453 9322 Z= 0.314 Chirality : 0.041 0.173 1006 Planarity : 0.004 0.031 1122 Dihedral : 9.579 56.585 968 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.76 % Allowed : 19.16 % Favored : 76.08 % 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: 1.36 (0.29), residues: 776 helix: 1.80 (0.20), residues: 578 sheet: None (None), residues: 0 loop : -1.91 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 514 HIS 0.002 0.001 HIS B 476 PHE 0.013 0.002 PHE A 610 TYR 0.029 0.002 TYR B 496 ARG 0.004 0.000 ARG B 448 Details of bonding type rmsd hydrogen bonds : bond 0.04929 ( 456) hydrogen bonds : angle 4.29980 ( 1368) SS BOND : bond 0.00017 ( 2) SS BOND : angle 0.03962 ( 4) covalent geometry : bond 0.00312 ( 6866) covalent geometry : angle 0.60803 ( 9318) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.710 Fit side-chains REVERT: A 253 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8709 (mm) REVERT: A 366 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.4566 (t80) REVERT: A 550 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: A 570 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8109 (mmt180) REVERT: A 622 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7524 (mm-30) REVERT: A 623 PHE cc_start: 0.6609 (m-80) cc_final: 0.6301 (m-10) REVERT: B 253 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8711 (mm) REVERT: B 366 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.4563 (t80) REVERT: B 570 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8098 (mmt180) REVERT: B 622 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: B 623 PHE cc_start: 0.6622 (m-80) cc_final: 0.6311 (m-10) outliers start: 33 outliers final: 10 residues processed: 132 average time/residue: 1.1039 time to fit residues: 154.2812 Evaluate side-chains 129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 570 ARG Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 452 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 618 ASN B 294 GLN B 452 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 618 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.172457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.128891 restraints weight = 7831.086| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.27 r_work: 0.3364 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6868 Z= 0.171 Angle : 0.636 9.176 9322 Z= 0.328 Chirality : 0.042 0.172 1006 Planarity : 0.004 0.031 1122 Dihedral : 9.642 56.750 968 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.47 % Allowed : 20.03 % Favored : 75.50 % 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: 1.24 (0.29), residues: 776 helix: 1.73 (0.20), residues: 568 sheet: None (None), residues: 0 loop : -1.83 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 514 HIS 0.003 0.001 HIS A 616 PHE 0.015 0.002 PHE B 391 TYR 0.026 0.002 TYR B 496 ARG 0.004 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.05144 ( 456) hydrogen bonds : angle 4.38881 ( 1368) SS BOND : bond 0.00023 ( 2) SS BOND : angle 0.03335 ( 4) covalent geometry : bond 0.00387 ( 6866) covalent geometry : angle 0.63650 ( 9318) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.802 Fit side-chains REVERT: A 310 ASN cc_start: 0.7683 (p0) cc_final: 0.7410 (p0) REVERT: A 366 PHE cc_start: 0.6389 (OUTLIER) cc_final: 0.4538 (t80) REVERT: A 369 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6743 (mttt) REVERT: A 495 LEU cc_start: 0.8770 (mt) cc_final: 0.8536 (mp) REVERT: A 550 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: A 622 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7425 (mm-30) REVERT: A 623 PHE cc_start: 0.6650 (m-80) cc_final: 0.6349 (m-10) REVERT: B 310 ASN cc_start: 0.7679 (p0) cc_final: 0.7408 (p0) REVERT: B 366 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.4538 (t80) REVERT: B 369 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6733 (mttt) REVERT: B 495 LEU cc_start: 0.8771 (mt) cc_final: 0.8536 (mp) REVERT: B 622 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: B 623 PHE cc_start: 0.6661 (m-80) cc_final: 0.6358 (m-10) outliers start: 31 outliers final: 9 residues processed: 126 average time/residue: 1.2671 time to fit residues: 168.9530 Evaluate side-chains 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 48 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 608 ASN A 618 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 608 ASN B 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.173165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129981 restraints weight = 7832.041| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.27 r_work: 0.3381 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6868 Z= 0.152 Angle : 0.637 8.941 9322 Z= 0.327 Chirality : 0.042 0.218 1006 Planarity : 0.003 0.032 1122 Dihedral : 9.120 58.827 960 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.31 % Allowed : 20.61 % Favored : 76.08 % 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: 1.23 (0.29), residues: 776 helix: 1.67 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -1.75 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 514 HIS 0.002 0.001 HIS B 476 PHE 0.014 0.002 PHE A 610 TYR 0.019 0.002 TYR B 496 ARG 0.004 0.000 ARG B 448 Details of bonding type rmsd hydrogen bonds : bond 0.05064 ( 456) hydrogen bonds : angle 4.39046 ( 1368) SS BOND : bond 0.00016 ( 2) SS BOND : angle 0.05571 ( 4) covalent geometry : bond 0.00338 ( 6866) covalent geometry : angle 0.63685 ( 9318) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.087 Fit side-chains REVERT: A 366 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.4623 (t80) REVERT: A 369 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6764 (mttt) REVERT: A 495 LEU cc_start: 0.8784 (mt) cc_final: 0.8519 (mp) REVERT: A 622 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7487 (mm-30) REVERT: A 623 PHE cc_start: 0.6801 (m-80) cc_final: 0.6383 (m-10) REVERT: B 366 PHE cc_start: 0.6132 (OUTLIER) cc_final: 0.4627 (t80) REVERT: B 369 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6759 (mttt) REVERT: B 495 LEU cc_start: 0.8783 (mt) cc_final: 0.8520 (mp) REVERT: B 622 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: B 623 PHE cc_start: 0.6810 (m-80) cc_final: 0.6391 (m-10) outliers start: 23 outliers final: 8 residues processed: 125 average time/residue: 1.1548 time to fit residues: 152.7871 Evaluate side-chains 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.0470 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 618 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 618 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.172838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129603 restraints weight = 7922.152| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.29 r_work: 0.3375 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6868 Z= 0.156 Angle : 0.643 9.114 9322 Z= 0.329 Chirality : 0.043 0.211 1006 Planarity : 0.004 0.032 1122 Dihedral : 9.119 59.837 960 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.03 % Allowed : 19.16 % Favored : 77.81 % 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: 1.19 (0.29), residues: 776 helix: 1.69 (0.20), residues: 568 sheet: None (None), residues: 0 loop : -1.80 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 573 HIS 0.002 0.001 HIS A 476 PHE 0.014 0.002 PHE A 391 TYR 0.021 0.002 TYR A 496 ARG 0.004 0.000 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 456) hydrogen bonds : angle 4.42999 ( 1368) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.07960 ( 4) covalent geometry : bond 0.00353 ( 6866) covalent geometry : angle 0.64342 ( 9318) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.707 Fit side-chains REVERT: A 366 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.4613 (t80) REVERT: A 369 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6760 (mttt) REVERT: A 495 LEU cc_start: 0.8800 (mt) cc_final: 0.8511 (mp) REVERT: A 496 TYR cc_start: 0.7758 (t80) cc_final: 0.7557 (t80) REVERT: A 622 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7395 (mm-30) REVERT: A 623 PHE cc_start: 0.6980 (m-80) cc_final: 0.6451 (m-10) REVERT: B 366 PHE cc_start: 0.6053 (OUTLIER) cc_final: 0.4614 (t80) REVERT: B 369 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6760 (mttt) REVERT: B 495 LEU cc_start: 0.8803 (mt) cc_final: 0.8515 (mp) REVERT: B 496 TYR cc_start: 0.7763 (t80) cc_final: 0.7562 (t80) REVERT: B 622 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7446 (mm-30) REVERT: B 623 PHE cc_start: 0.6991 (m-80) cc_final: 0.6462 (m-10) outliers start: 21 outliers final: 8 residues processed: 117 average time/residue: 1.0234 time to fit residues: 126.9817 Evaluate side-chains 124 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.1980 chunk 23 optimal weight: 0.4980 chunk 55 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 608 ASN A 618 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 608 ASN B 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.174355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.131407 restraints weight = 7819.954| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.27 r_work: 0.3398 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6868 Z= 0.145 Angle : 0.631 9.438 9322 Z= 0.323 Chirality : 0.042 0.194 1006 Planarity : 0.004 0.032 1122 Dihedral : 8.982 58.301 960 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.45 % Allowed : 20.32 % Favored : 77.23 % 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: 1.30 (0.29), residues: 776 helix: 1.73 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -1.72 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 573 HIS 0.002 0.001 HIS B 476 PHE 0.014 0.001 PHE B 610 TYR 0.026 0.002 TYR B 496 ARG 0.004 0.000 ARG B 448 Details of bonding type rmsd hydrogen bonds : bond 0.04841 ( 456) hydrogen bonds : angle 4.38994 ( 1368) SS BOND : bond 0.00006 ( 2) SS BOND : angle 0.15772 ( 4) covalent geometry : bond 0.00322 ( 6866) covalent geometry : angle 0.63075 ( 9318) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5469.84 seconds wall clock time: 96 minutes 12.54 seconds (5772.54 seconds total)