Starting phenix.real_space_refine on Tue Feb 11 05:13:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ikj_35514/02_2025/8ikj_35514.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ikj_35514/02_2025/8ikj_35514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ikj_35514/02_2025/8ikj_35514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ikj_35514/02_2025/8ikj_35514.map" model { file = "/net/cci-nas-00/data/ceres_data/8ikj_35514/02_2025/8ikj_35514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ikj_35514/02_2025/8ikj_35514.cif" } resolution = 3.2 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= 0.013 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 2712 2.51 5 N 702 2.21 5 O 758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4200 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 4158 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 532, 4147 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 20, 'TRANS': 511} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 532, 4147 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 20, 'TRANS': 511} Chain breaks: 1 bond proxies already assigned to first conformer: 4226 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.00, per 1000 atoms: 1.19 Number of scatterers: 4200 At special positions: 0 Unit cell: (79.98, 92.07, 119.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 758 8.00 N 702 7.00 C 2712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 495 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 513 " - pdb=" SG CYS R 527 " distance=2.03 Simple disulfide: pdb=" SG CYS R 612 " - pdb=" SG CYS R 684 " 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 Links applied NAG-ASN " NAG R 901 " - " ASN R 413 " " NAG R 902 " - " ASN R 406 " " NAG R 903 " - " ASN R 520 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 982.6 milliseconds 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 988 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 3 sheets defined 52.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'R' and resid 272 through 289 Processing helix chain 'R' and resid 293 through 311 Processing helix chain 'R' and resid 319 through 343 removed outlier: 3.814A pdb=" N LYS R 343 " --> pdb=" O ARG R 339 " (cutoff:3.500A) Processing helix chain 'R' and resid 385 through 390 removed outlier: 3.531A pdb=" N ALA R 389 " --> pdb=" O TRP R 385 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY R 390 " --> pdb=" O ALA R 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 385 through 390' Processing helix chain 'R' and resid 406 through 410 Processing helix chain 'R' and resid 419 through 431 Processing helix chain 'R' and resid 548 through 572 Processing helix chain 'R' and resid 577 through 601 Processing helix chain 'R' and resid 609 through 643 Processing helix chain 'R' and resid 651 through 674 Proline residue: R 663 - end of helix Processing helix chain 'R' and resid 691 through 719 removed outlier: 3.675A pdb=" N SER R 695 " --> pdb=" O GLY R 691 " (cutoff:3.500A) Proline residue: R 699 - end of helix Processing helix chain 'R' and resid 735 through 756 Processing helix chain 'R' and resid 766 through 787 removed outlier: 3.610A pdb=" N VAL R 770 " --> pdb=" O VAL R 766 " (cutoff:3.500A) Processing helix chain 'R' and resid 790 through 801 removed outlier: 3.572A pdb=" N ARG R 794 " --> pdb=" O ASN R 790 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 348 through 353 removed outlier: 3.666A pdb=" N GLN R 365 " --> pdb=" O ALA R 397 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL R 398 " --> pdb=" O LEU R 450 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU R 450 " --> pdb=" O VAL R 398 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY R 400 " --> pdb=" O ILE R 448 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE R 448 " --> pdb=" O GLY R 400 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU R 402 " --> pdb=" O ASN R 446 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 371 through 374 removed outlier: 3.782A pdb=" N GLY R 517 " --> pdb=" O THR R 524 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN R 526 " --> pdb=" O VAL R 515 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL R 515 " --> pdb=" O GLN R 526 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 436 through 438 removed outlier: 4.520A pdb=" N SER R 532 " --> pdb=" O TRP R 498 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA R 538 " --> pdb=" O GLU R 492 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU R 492 " --> pdb=" O ALA R 538 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 749 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: 1.23 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1088 1.33 - 1.46: 869 1.46 - 1.58: 2301 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 4296 Sorted by residual: bond pdb=" C ALA R 412 " pdb=" N ASN R 413 " ideal model delta sigma weight residual 1.332 1.576 -0.244 1.40e-02 5.10e+03 3.03e+02 bond pdb=" C LYS R 519 " pdb=" N ASN R 520 " ideal model delta sigma weight residual 1.333 1.444 -0.111 1.39e-02 5.18e+03 6.42e+01 bond pdb=" C GLN R 405 " pdb=" N ASN R 406 " ideal model delta sigma weight residual 1.330 1.269 0.061 1.52e-02 4.33e+03 1.60e+01 bond pdb=" C ASN R 406 " pdb=" N MET R 407 " ideal model delta sigma weight residual 1.335 1.363 -0.029 1.33e-02 5.65e+03 4.74e+00 bond pdb=" C ASN R 520 " pdb=" N GLY R 521 " ideal model delta sigma weight residual 1.331 1.304 0.027 1.32e-02 5.74e+03 4.17e+00 ... (remaining 4291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 5680 1.88 - 3.76: 126 3.76 - 5.63: 25 5.63 - 7.51: 2 7.51 - 9.39: 4 Bond angle restraints: 5837 Sorted by residual: angle pdb=" CA GLN R 405 " pdb=" C GLN R 405 " pdb=" N ASN R 406 " ideal model delta sigma weight residual 118.21 126.57 -8.36 1.36e+00 5.41e-01 3.78e+01 angle pdb=" O GLN R 405 " pdb=" C GLN R 405 " pdb=" N ASN R 406 " ideal model delta sigma weight residual 122.46 114.48 7.98 1.37e+00 5.33e-01 3.40e+01 angle pdb=" C GLY R 647 " pdb=" N GLN R 648 " pdb=" CA GLN R 648 " ideal model delta sigma weight residual 121.54 129.73 -8.19 1.91e+00 2.74e-01 1.84e+01 angle pdb=" CA LEU R 549 " pdb=" CB LEU R 549 " pdb=" CG LEU R 549 " ideal model delta sigma weight residual 116.30 125.69 -9.39 3.50e+00 8.16e-02 7.20e+00 angle pdb=" CA MET R 537 " pdb=" CB MET R 537 " pdb=" CG MET R 537 " ideal model delta sigma weight residual 114.10 119.44 -5.34 2.00e+00 2.50e-01 7.13e+00 ... (remaining 5832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.04: 2306 14.04 - 28.08: 193 28.08 - 42.11: 61 42.11 - 56.15: 14 56.15 - 70.18: 6 Dihedral angle restraints: 2580 sinusoidal: 1048 harmonic: 1532 Sorted by residual: dihedral pdb=" CA ASP R 761 " pdb=" C ASP R 761 " pdb=" N ASP R 762 " pdb=" CA ASP R 762 " ideal model delta harmonic sigma weight residual -180.00 -160.47 -19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA MET R 537 " pdb=" C MET R 537 " pdb=" N ALA R 538 " pdb=" CA ALA R 538 " ideal model delta harmonic sigma weight residual 180.00 -160.97 -19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB CYS R 612 " pdb=" SG CYS R 612 " pdb=" SG CYS R 684 " pdb=" CB CYS R 684 " ideal model delta sinusoidal sigma weight residual -86.00 -116.85 30.85 1 1.00e+01 1.00e-02 1.36e+01 ... (remaining 2577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 684 0.302 - 0.603: 0 0.603 - 0.905: 0 0.905 - 1.206: 1 1.206 - 1.508: 1 Chirality restraints: 686 Sorted by residual: chirality pdb=" C1 NAG R 902 " pdb=" ND2 ASN R 406 " pdb=" C2 NAG R 902 " pdb=" O5 NAG R 902 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-01 2.50e+01 5.68e+01 chirality pdb=" C1 NAG R 903 " pdb=" ND2 ASN R 520 " pdb=" C2 NAG R 903 " pdb=" O5 NAG R 903 " both_signs ideal model delta sigma weight residual False -2.40 -1.35 -1.05 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" CA MET R 537 " pdb=" N MET R 537 " pdb=" C MET R 537 " pdb=" CB MET R 537 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.48e-01 ... (remaining 683 not shown) Planarity restraints: 727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 413 " -0.128 2.00e-02 2.50e+03 1.43e-01 2.55e+02 pdb=" CG ASN R 413 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN R 413 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN R 413 " 0.228 2.00e-02 2.50e+03 pdb=" C1 NAG R 901 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 348 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C GLY R 348 " -0.052 2.00e-02 2.50e+03 pdb=" O GLY R 348 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO R 349 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA R 319 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO R 320 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO R 320 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 320 " -0.039 5.00e-02 4.00e+02 ... (remaining 724 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 106 2.71 - 3.26: 4103 3.26 - 3.80: 6903 3.80 - 4.35: 8293 4.35 - 4.90: 14231 Nonbonded interactions: 33636 Sorted by model distance: nonbonded pdb=" O ARG R 643 " pdb=" NE2 GLN R 646 " model vdw 2.162 3.120 nonbonded pdb=" OG1 THR R 568 " pdb=" OH TYR R 797 " model vdw 2.181 3.040 nonbonded pdb=" O SER R 356 " pdb=" NE2 GLN R 405 " model vdw 2.201 3.120 nonbonded pdb=" NH1 ARG R 490 " pdb=" O GLY R 605 " model vdw 2.203 3.120 nonbonded pdb=" OE1 GLU R 295 " pdb=" NE2 GLN R 299 " model vdw 2.215 3.120 ... (remaining 33631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 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: 0.720 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 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 0.244 4296 Z= 0.341 Angle : 0.697 9.389 5837 Z= 0.369 Chirality : 0.083 1.508 686 Planarity : 0.006 0.071 724 Dihedral : 12.439 70.184 1583 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 1.60 (0.36), residues: 529 helix: 2.40 (0.31), residues: 266 sheet: 0.66 (0.58), residues: 78 loop : -0.79 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 498 HIS 0.002 0.000 HIS R 585 PHE 0.015 0.001 PHE R 627 TYR 0.009 0.001 TYR R 769 ARG 0.014 0.001 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.7964 (mtm) cc_final: 0.7721 (mtm) REVERT: R 338 MET cc_start: 0.8201 (mtm) cc_final: 0.7958 (mtm) REVERT: R 491 GLN cc_start: 0.6827 (tm-30) cc_final: 0.6241 (tm-30) REVERT: R 537 MET cc_start: 0.5740 (tpt) cc_final: 0.5456 (tpt) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3115 time to fit residues: 29.7498 Evaluate side-chains 76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 40.0000 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 HIS R 299 GLN R 646 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.174905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.121903 restraints weight = 10495.850| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.56 r_work: 0.3344 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 4296 Z= 0.373 Angle : 0.706 12.433 5837 Z= 0.352 Chirality : 0.046 0.303 686 Planarity : 0.005 0.060 724 Dihedral : 5.112 37.506 632 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.32 % Allowed : 5.92 % Favored : 92.76 % 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 (0.36), residues: 529 helix: 1.88 (0.30), residues: 269 sheet: 0.35 (0.59), residues: 84 loop : -0.37 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 498 HIS 0.003 0.001 HIS R 539 PHE 0.017 0.002 PHE R 627 TYR 0.014 0.002 TYR R 660 ARG 0.007 0.001 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8466 (mtm) cc_final: 0.8190 (mtm) REVERT: R 338 MET cc_start: 0.8569 (mtm) cc_final: 0.8265 (mtm) REVERT: R 407 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6982 (mmp) REVERT: R 491 GLN cc_start: 0.7267 (tm-30) cc_final: 0.6883 (tm-30) REVERT: R 537 MET cc_start: 0.6443 (tpt) cc_final: 0.5864 (tpt) REVERT: R 540 TYR cc_start: 0.7683 (m-10) cc_final: 0.7354 (m-10) REVERT: R 544 ASP cc_start: 0.6806 (p0) cc_final: 0.6555 (p0) REVERT: R 576 GLN cc_start: 0.7358 (mm110) cc_final: 0.7039 (mm110) REVERT: R 689 GLU cc_start: 0.6814 (tp30) cc_final: 0.6584 (tp30) REVERT: R 792 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8330 (mtpp) outliers start: 6 outliers final: 3 residues processed: 83 average time/residue: 0.2645 time to fit residues: 25.5344 Evaluate side-chains 81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 21 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 42 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.176693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.125988 restraints weight = 15940.115| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 4.38 r_work: 0.3306 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4296 Z= 0.235 Angle : 0.634 10.691 5837 Z= 0.317 Chirality : 0.042 0.219 686 Planarity : 0.005 0.055 724 Dihedral : 5.072 45.611 632 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.32 % Allowed : 6.80 % Favored : 91.89 % 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: 1.57 (0.37), residues: 529 helix: 2.22 (0.31), residues: 262 sheet: 0.44 (0.60), residues: 80 loop : -0.35 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 498 HIS 0.004 0.001 HIS R 539 PHE 0.013 0.001 PHE R 627 TYR 0.007 0.001 TYR R 621 ARG 0.002 0.000 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8523 (mtm) cc_final: 0.8223 (mtm) REVERT: R 338 MET cc_start: 0.8655 (mtm) cc_final: 0.8319 (mtm) REVERT: R 407 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7089 (mmp) REVERT: R 423 GLN cc_start: 0.8729 (mt0) cc_final: 0.8515 (mt0) REVERT: R 491 GLN cc_start: 0.7342 (tm-30) cc_final: 0.6965 (tm-30) REVERT: R 537 MET cc_start: 0.6364 (tpt) cc_final: 0.5969 (tpt) REVERT: R 540 TYR cc_start: 0.7776 (m-10) cc_final: 0.7439 (m-10) REVERT: R 576 GLN cc_start: 0.7470 (mm110) cc_final: 0.7099 (mm110) REVERT: R 792 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8429 (mtpp) outliers start: 6 outliers final: 3 residues processed: 85 average time/residue: 0.2757 time to fit residues: 27.1587 Evaluate side-chains 82 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 440 ARG Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 778 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.176501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.129005 restraints weight = 9999.611| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.01 r_work: 0.3395 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4296 Z= 0.330 Angle : 0.662 10.389 5837 Z= 0.334 Chirality : 0.042 0.182 686 Planarity : 0.005 0.054 724 Dihedral : 4.950 40.808 632 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.32 % Allowed : 7.89 % Favored : 90.79 % 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 (0.37), residues: 529 helix: 1.82 (0.31), residues: 268 sheet: 0.45 (0.61), residues: 80 loop : -0.41 (0.47), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 498 HIS 0.002 0.000 HIS R 585 PHE 0.022 0.002 PHE R 623 TYR 0.010 0.002 TYR R 769 ARG 0.010 0.001 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8442 (mtm) cc_final: 0.8147 (mtm) REVERT: R 338 MET cc_start: 0.8462 (mtm) cc_final: 0.8177 (mtm) REVERT: R 407 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.7085 (mmp) REVERT: R 491 GLN cc_start: 0.7250 (tm-30) cc_final: 0.6674 (tm-30) REVERT: R 537 MET cc_start: 0.6142 (tpt) cc_final: 0.5912 (tpt) REVERT: R 540 TYR cc_start: 0.7724 (m-10) cc_final: 0.7410 (m-10) REVERT: R 544 ASP cc_start: 0.6605 (p0) cc_final: 0.6258 (p0) REVERT: R 576 GLN cc_start: 0.7357 (mm110) cc_final: 0.7054 (mm110) REVERT: R 693 LEU cc_start: 0.8109 (tp) cc_final: 0.7902 (tp) REVERT: R 792 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8420 (mtpp) outliers start: 6 outliers final: 3 residues processed: 81 average time/residue: 0.2601 time to fit residues: 24.6926 Evaluate side-chains 80 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.176158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.127725 restraints weight = 10473.127| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.13 r_work: 0.3402 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4296 Z= 0.250 Angle : 0.676 11.146 5837 Z= 0.335 Chirality : 0.041 0.192 686 Planarity : 0.004 0.054 724 Dihedral : 4.759 37.160 632 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.10 % Allowed : 9.21 % Favored : 89.69 % 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: 1.41 (0.37), residues: 529 helix: 2.11 (0.31), residues: 262 sheet: 0.25 (0.60), residues: 80 loop : -0.41 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 498 HIS 0.003 0.000 HIS R 539 PHE 0.024 0.002 PHE R 623 TYR 0.008 0.001 TYR R 769 ARG 0.004 0.000 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8415 (mtm) cc_final: 0.8163 (mtm) REVERT: R 338 MET cc_start: 0.8493 (mtm) cc_final: 0.8190 (mtm) REVERT: R 407 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6713 (mmp) REVERT: R 491 GLN cc_start: 0.7202 (tm-30) cc_final: 0.6544 (tm-30) REVERT: R 537 MET cc_start: 0.6097 (tpt) cc_final: 0.5811 (tpt) REVERT: R 540 TYR cc_start: 0.7756 (m-10) cc_final: 0.7418 (m-10) REVERT: R 544 ASP cc_start: 0.6608 (p0) cc_final: 0.6296 (p0) REVERT: R 576 GLN cc_start: 0.7385 (mm110) cc_final: 0.7055 (mm110) REVERT: R 792 LYS cc_start: 0.8728 (mtpp) cc_final: 0.8420 (mtpp) outliers start: 5 outliers final: 4 residues processed: 80 average time/residue: 0.2826 time to fit residues: 26.4654 Evaluate side-chains 81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 784 LEU Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 0.0170 chunk 45 optimal weight: 0.0980 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.176613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.122742 restraints weight = 17164.208| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 4.58 r_work: 0.3338 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4296 Z= 0.218 Angle : 0.665 11.029 5837 Z= 0.330 Chirality : 0.041 0.179 686 Planarity : 0.004 0.053 724 Dihedral : 4.480 25.621 632 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.32 % Allowed : 9.87 % Favored : 88.82 % 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: 1.51 (0.37), residues: 529 helix: 2.27 (0.31), residues: 262 sheet: 0.44 (0.61), residues: 74 loop : -0.56 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 498 HIS 0.003 0.000 HIS R 539 PHE 0.022 0.001 PHE R 623 TYR 0.007 0.001 TYR R 769 ARG 0.003 0.000 ARG R 613 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8475 (mtm) cc_final: 0.8195 (mtm) REVERT: R 338 MET cc_start: 0.8581 (mtm) cc_final: 0.8262 (mtm) REVERT: R 407 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6687 (mmp) REVERT: R 491 GLN cc_start: 0.7256 (tm-30) cc_final: 0.6534 (tm-30) REVERT: R 537 MET cc_start: 0.6270 (tpt) cc_final: 0.5961 (tpt) REVERT: R 540 TYR cc_start: 0.7844 (m-10) cc_final: 0.7524 (m-10) REVERT: R 544 ASP cc_start: 0.6749 (p0) cc_final: 0.6469 (p0) REVERT: R 576 GLN cc_start: 0.7512 (mm110) cc_final: 0.7154 (mm110) REVERT: R 630 MET cc_start: 0.7766 (tpt) cc_final: 0.6944 (tpt) REVERT: R 792 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8393 (mtpp) outliers start: 6 outliers final: 4 residues processed: 81 average time/residue: 0.2757 time to fit residues: 25.9635 Evaluate side-chains 81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 784 LEU Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.175807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.127043 restraints weight = 11917.516| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.66 r_work: 0.3370 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4296 Z= 0.307 Angle : 0.692 10.974 5837 Z= 0.345 Chirality : 0.042 0.163 686 Planarity : 0.004 0.053 724 Dihedral : 4.453 22.568 632 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.10 % Allowed : 11.18 % Favored : 87.72 % 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 (0.36), residues: 529 helix: 2.05 (0.31), residues: 262 sheet: 0.55 (0.62), residues: 73 loop : -0.55 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 498 HIS 0.002 0.000 HIS R 539 PHE 0.022 0.002 PHE R 623 TYR 0.009 0.001 TYR R 769 ARG 0.008 0.001 ARG R 435 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8462 (mtm) cc_final: 0.8184 (mtm) REVERT: R 338 MET cc_start: 0.8553 (mtm) cc_final: 0.8225 (mtm) REVERT: R 407 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6671 (mmp) REVERT: R 491 GLN cc_start: 0.7204 (tm-30) cc_final: 0.6460 (tm-30) REVERT: R 537 MET cc_start: 0.6244 (tpt) cc_final: 0.5936 (tpt) REVERT: R 544 ASP cc_start: 0.6749 (p0) cc_final: 0.6375 (p0) REVERT: R 576 GLN cc_start: 0.7448 (mm110) cc_final: 0.7100 (mm110) REVERT: R 792 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8429 (mtpp) outliers start: 5 outliers final: 4 residues processed: 79 average time/residue: 0.2799 time to fit residues: 25.6534 Evaluate side-chains 80 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 784 LEU Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 19 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.176132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.125677 restraints weight = 15566.446| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 4.31 r_work: 0.3333 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 0.005 0.048 4296 Z= 0.309 Angle : 0.726 11.150 5837 Z= 0.360 Chirality : 0.042 0.153 686 Planarity : 0.005 0.052 724 Dihedral : 4.510 23.000 632 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.10 % Allowed : 11.18 % Favored : 87.72 % 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 (0.36), residues: 529 helix: 2.07 (0.31), residues: 262 sheet: 0.56 (0.63), residues: 73 loop : -0.58 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 498 HIS 0.001 0.000 HIS R 539 PHE 0.022 0.002 PHE R 623 TYR 0.009 0.001 TYR R 769 ARG 0.012 0.001 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8545 (mtm) cc_final: 0.8247 (mtm) REVERT: R 338 MET cc_start: 0.8619 (mtm) cc_final: 0.8282 (mtm) REVERT: R 407 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6716 (mmp) REVERT: R 491 GLN cc_start: 0.7233 (tm-30) cc_final: 0.6500 (tm-30) REVERT: R 537 MET cc_start: 0.6330 (tpt) cc_final: 0.5962 (tpt) REVERT: R 543 GLU cc_start: 0.7388 (pm20) cc_final: 0.7160 (pm20) REVERT: R 576 GLN cc_start: 0.7543 (mm110) cc_final: 0.7191 (mm110) REVERT: R 693 LEU cc_start: 0.8083 (tp) cc_final: 0.7877 (tp) outliers start: 5 outliers final: 4 residues processed: 77 average time/residue: 0.2809 time to fit residues: 25.2572 Evaluate side-chains 77 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 784 LEU Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 745 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.176511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.124389 restraints weight = 9834.221| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.38 r_work: 0.3408 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4296 Z= 0.312 Angle : 0.728 11.274 5837 Z= 0.362 Chirality : 0.043 0.174 686 Planarity : 0.005 0.063 724 Dihedral : 4.465 22.706 632 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.54 % Allowed : 10.96 % Favored : 87.50 % 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: 1.42 (0.37), residues: 529 helix: 2.10 (0.31), residues: 262 sheet: 0.65 (0.64), residues: 73 loop : -0.56 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 498 HIS 0.002 0.000 HIS R 539 PHE 0.023 0.002 PHE R 623 TYR 0.011 0.002 TYR R 683 ARG 0.014 0.001 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8403 (mtm) cc_final: 0.8131 (mtm) REVERT: R 338 MET cc_start: 0.8537 (mtm) cc_final: 0.8205 (mtm) REVERT: R 407 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6548 (mmp) REVERT: R 491 GLN cc_start: 0.7213 (tm-30) cc_final: 0.6443 (tm-30) REVERT: R 537 MET cc_start: 0.6186 (tpt) cc_final: 0.5895 (tpt) REVERT: R 543 GLU cc_start: 0.7194 (pm20) cc_final: 0.6990 (pm20) REVERT: R 576 GLN cc_start: 0.7391 (mm110) cc_final: 0.7061 (mm110) outliers start: 7 outliers final: 6 residues processed: 77 average time/residue: 0.2602 time to fit residues: 23.3513 Evaluate side-chains 79 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 630 MET Chi-restraints excluded: chain R residue 745 GLN Chi-restraints excluded: chain R residue 784 LEU Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 19 optimal weight: 0.0020 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 745 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.178121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131671 restraints weight = 10352.932| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.21 r_work: 0.3419 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4296 Z= 0.241 Angle : 0.749 18.195 5837 Z= 0.359 Chirality : 0.042 0.175 686 Planarity : 0.005 0.063 724 Dihedral : 4.403 22.724 632 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.54 % Allowed : 11.18 % Favored : 87.28 % 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: 1.45 (0.37), residues: 529 helix: 2.19 (0.31), residues: 262 sheet: 0.37 (0.61), residues: 75 loop : -0.51 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 498 HIS 0.002 0.000 HIS R 539 PHE 0.023 0.002 PHE R 623 TYR 0.011 0.001 TYR R 683 ARG 0.014 0.001 ARG R 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 309 MET cc_start: 0.8420 (mtm) cc_final: 0.8138 (mtm) REVERT: R 338 MET cc_start: 0.8552 (mtm) cc_final: 0.8228 (mtm) REVERT: R 407 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6538 (mmp) REVERT: R 491 GLN cc_start: 0.7121 (tm-30) cc_final: 0.6309 (tm-30) REVERT: R 537 MET cc_start: 0.6088 (tpt) cc_final: 0.5788 (tpt) REVERT: R 576 GLN cc_start: 0.7395 (mm110) cc_final: 0.7046 (mm110) REVERT: R 792 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8466 (mttm) outliers start: 7 outliers final: 6 residues processed: 72 average time/residue: 0.2897 time to fit residues: 24.1846 Evaluate side-chains 76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 548 THR Chi-restraints excluded: chain R residue 551 THR Chi-restraints excluded: chain R residue 630 MET Chi-restraints excluded: chain R residue 745 GLN Chi-restraints excluded: chain R residue 784 LEU Chi-restraints excluded: chain R residue 791 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 37 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 13 optimal weight: 0.0070 chunk 36 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.178066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.127819 restraints weight = 7261.253| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.73 r_work: 0.3474 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.246 4296 Z= 0.463 Angle : 1.254 59.160 5837 Z= 0.722 Chirality : 0.044 0.433 686 Planarity : 0.005 0.062 724 Dihedral : 4.461 22.722 632 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.54 % Allowed : 11.40 % Favored : 87.06 % Cbeta Deviations : 0.20 % 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: 1.42 (0.37), residues: 529 helix: 2.15 (0.31), residues: 262 sheet: 0.37 (0.61), residues: 75 loop : -0.51 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 498 HIS 0.002 0.000 HIS R 539 PHE 0.022 0.001 PHE R 623 TYR 0.010 0.001 TYR R 683 ARG 0.013 0.001 ARG R 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3255.02 seconds wall clock time: 58 minutes 2.81 seconds (3482.81 seconds total)