Starting phenix.real_space_refine on Thu Jun 5 18:51:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wwk_32868/06_2025/7wwk_32868.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwk_32868/06_2025/7wwk_32868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wwk_32868/06_2025/7wwk_32868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwk_32868/06_2025/7wwk_32868.map" model { file = "/net/cci-nas-00/data/ceres_data/7wwk_32868/06_2025/7wwk_32868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwk_32868/06_2025/7wwk_32868.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.028 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 30 5.16 5 C 4214 2.51 5 N 1116 2.21 5 O 1260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6620 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1550 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "C" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Time building chain proxies: 6.42, per 1000 atoms: 0.97 Number of scatterers: 6620 At special positions: 0 Unit cell: (95.12, 107.42, 107.42, 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 30 16.00 O 1260 8.00 N 1116 7.00 C 4214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " 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: 1.60 Conformation dependent library (CDL) restraints added in 990.1 milliseconds 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1558 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 18 sheets defined 10.2% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.615A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.527A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.909A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.571A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.137A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.560A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.945A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.764A pdb=" N SER G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.144A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.158A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.142A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.287A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.542A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.583A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.547A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.651A pdb=" N PHE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE G 57 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.646A pdb=" N ASP G 110 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.561A pdb=" N ALA H 13 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 12 removed outlier: 8.673A pdb=" N TYR I 32 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE I 52 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.623A pdb=" N ASP I 110 " --> pdb=" O ARG I 98 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.93 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: 1912 1.33 - 1.45: 1282 1.45 - 1.57: 3560 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 6790 Sorted by residual: bond pdb=" C PHE C 392 " pdb=" N THR C 393 " ideal model delta sigma weight residual 1.335 1.403 -0.068 1.34e-02 5.57e+03 2.57e+01 bond pdb=" C CYS C 391 " pdb=" N PHE C 392 " ideal model delta sigma weight residual 1.331 1.390 -0.060 1.36e-02 5.41e+03 1.92e+01 bond pdb=" N CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sigma weight residual 1.454 1.493 -0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" N VAL B 341 " pdb=" CA VAL B 341 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.08e-02 8.57e+03 1.00e+01 bond pdb=" N LEU B 390 " pdb=" CA LEU B 390 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.25e-02 6.40e+03 8.29e+00 ... (remaining 6785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 8766 1.56 - 3.11: 378 3.11 - 4.67: 69 4.67 - 6.22: 3 6.22 - 7.78: 3 Bond angle restraints: 9219 Sorted by residual: angle pdb=" N VAL B 341 " pdb=" CA VAL B 341 " pdb=" C VAL B 341 " ideal model delta sigma weight residual 113.42 108.77 4.65 1.17e+00 7.31e-01 1.58e+01 angle pdb=" CA GLY G 99 " pdb=" C GLY G 99 " pdb=" O GLY G 99 " ideal model delta sigma weight residual 122.03 117.63 4.40 1.15e+00 7.56e-01 1.47e+01 angle pdb=" CA VAL I 107 " pdb=" C VAL I 107 " pdb=" O VAL I 107 " ideal model delta sigma weight residual 122.13 117.97 4.16 1.11e+00 8.12e-01 1.41e+01 angle pdb=" CA VAL B 524 " pdb=" C VAL B 524 " pdb=" O VAL B 524 " ideal model delta sigma weight residual 121.70 117.79 3.91 1.06e+00 8.90e-01 1.36e+01 angle pdb=" N ASN B 388 " pdb=" CA ASN B 388 " pdb=" C ASN B 388 " ideal model delta sigma weight residual 112.72 108.55 4.17 1.14e+00 7.69e-01 1.34e+01 ... (remaining 9214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3659 18.00 - 35.99: 305 35.99 - 53.99: 42 53.99 - 71.99: 6 71.99 - 89.98: 5 Dihedral angle restraints: 4017 sinusoidal: 1564 harmonic: 2453 Sorted by residual: dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 88 " pdb=" CB CYS H 88 " ideal model delta sinusoidal sigma weight residual 93.00 154.02 -61.02 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 145.75 -52.75 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 130.83 -37.83 1 1.00e+01 1.00e-02 2.02e+01 ... (remaining 4014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 667 0.039 - 0.079: 199 0.079 - 0.118: 90 0.118 - 0.157: 27 0.157 - 0.196: 8 Chirality restraints: 991 Sorted by residual: chirality pdb=" CA ARG G 38 " pdb=" N ARG G 38 " pdb=" C ARG G 38 " pdb=" CB ARG G 38 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA VAL B 524 " pdb=" N VAL B 524 " pdb=" C VAL B 524 " pdb=" CB VAL B 524 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA VAL B 341 " pdb=" N VAL B 341 " pdb=" C VAL B 341 " pdb=" CB VAL B 341 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.74e-01 ... (remaining 988 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 526 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C GLY C 526 " -0.034 2.00e-02 2.50e+03 pdb=" O GLY C 526 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO C 527 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 523 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C THR B 523 " 0.033 2.00e-02 2.50e+03 pdb=" O THR B 523 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B 524 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 81 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" CG ASP H 81 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP H 81 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP H 81 " 0.011 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 518 2.74 - 3.28: 6207 3.28 - 3.82: 10069 3.82 - 4.36: 12376 4.36 - 4.90: 22292 Nonbonded interactions: 51462 Sorted by model distance: nonbonded pdb=" OG SER F 7 " pdb=" OG1 THR F 22 " model vdw 2.206 3.040 nonbonded pdb=" O GLY G 26 " pdb=" OH TYR G 32 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR F 36 " pdb=" OE1 GLN F 89 " model vdw 2.267 3.040 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 2.283 3.120 nonbonded pdb=" OH TYR H 36 " pdb=" OE1 GLN H 89 " model vdw 2.355 3.040 ... (remaining 51457 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and resid 335 through 527) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } 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: 11.490 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.860 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 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 0.068 6802 Z= 0.293 Angle : 0.712 7.777 9243 Z= 0.449 Chirality : 0.050 0.196 991 Planarity : 0.004 0.032 1184 Dihedral : 12.679 89.981 2423 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.08 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.93 (0.29), residues: 833 helix: -3.93 (0.45), residues: 57 sheet: 0.12 (0.29), residues: 334 loop : -0.67 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 36 HIS 0.004 0.001 HIS C 505 PHE 0.011 0.001 PHE C 347 TYR 0.011 0.001 TYR H 94 ARG 0.007 0.000 ARG I 87 Details of bonding type rmsd hydrogen bonds : bond 0.14457 ( 208) hydrogen bonds : angle 6.92539 ( 495) SS BOND : bond 0.00343 ( 12) SS BOND : angle 0.99174 ( 24) covalent geometry : bond 0.00452 ( 6790) covalent geometry : angle 0.71102 ( 9219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 418 ILE cc_start: 0.9361 (mm) cc_final: 0.9156 (mt) REVERT: G 54 ILE cc_start: 0.9025 (tp) cc_final: 0.8812 (tp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2189 time to fit residues: 44.7245 Evaluate side-chains 142 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.084031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.070911 restraints weight = 14086.312| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.67 r_work: 0.2829 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6802 Z= 0.174 Angle : 0.561 7.218 9243 Z= 0.296 Chirality : 0.046 0.140 991 Planarity : 0.004 0.032 1184 Dihedral : 4.264 15.472 935 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.21 % Allowed : 9.27 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.86 (0.29), residues: 833 helix: -3.83 (0.45), residues: 57 sheet: 0.09 (0.29), residues: 338 loop : -0.56 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 47 HIS 0.007 0.001 HIS C 505 PHE 0.012 0.001 PHE C 347 TYR 0.019 0.001 TYR H 94 ARG 0.005 0.000 ARG I 87 Details of bonding type rmsd hydrogen bonds : bond 0.03135 ( 208) hydrogen bonds : angle 5.76024 ( 495) SS BOND : bond 0.00207 ( 12) SS BOND : angle 0.88397 ( 24) covalent geometry : bond 0.00405 ( 6790) covalent geometry : angle 0.56027 ( 9219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 54 ILE cc_start: 0.9171 (tp) cc_final: 0.8782 (mm) REVERT: I 3 GLN cc_start: 0.7741 (pm20) cc_final: 0.7298 (pm20) REVERT: I 35 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9105 (mt) outliers start: 16 outliers final: 12 residues processed: 150 average time/residue: 0.2197 time to fit residues: 42.6743 Evaluate side-chains 152 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.085040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.071884 restraints weight = 14101.843| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.70 r_work: 0.2849 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6802 Z= 0.117 Angle : 0.515 7.219 9243 Z= 0.270 Chirality : 0.044 0.141 991 Planarity : 0.004 0.039 1184 Dihedral : 4.036 13.732 935 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.80 % Allowed : 12.86 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.29), residues: 833 helix: -4.08 (0.42), residues: 57 sheet: 0.09 (0.28), residues: 340 loop : -0.51 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 47 HIS 0.004 0.001 HIS C 505 PHE 0.015 0.001 PHE G 29 TYR 0.012 0.001 TYR H 94 ARG 0.008 0.000 ARG I 98 Details of bonding type rmsd hydrogen bonds : bond 0.02789 ( 208) hydrogen bonds : angle 5.52292 ( 495) SS BOND : bond 0.00305 ( 12) SS BOND : angle 0.99922 ( 24) covalent geometry : bond 0.00270 ( 6790) covalent geometry : angle 0.51295 ( 9219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 18 ARG cc_start: 0.8540 (ttm-80) cc_final: 0.8075 (ttt180) REVERT: G 54 ILE cc_start: 0.9168 (tp) cc_final: 0.8941 (tp) REVERT: H 108 ARG cc_start: 0.4901 (ptt-90) cc_final: 0.4540 (ptt90) REVERT: I 3 GLN cc_start: 0.7696 (pm20) cc_final: 0.7224 (pm20) REVERT: I 35 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9068 (mt) outliers start: 13 outliers final: 11 residues processed: 153 average time/residue: 0.2014 time to fit residues: 40.1379 Evaluate side-chains 147 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.084221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.071060 restraints weight = 14250.241| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.70 r_work: 0.2833 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6802 Z= 0.143 Angle : 0.526 7.055 9243 Z= 0.276 Chirality : 0.044 0.145 991 Planarity : 0.003 0.031 1184 Dihedral : 4.116 14.233 935 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.04 % Allowed : 13.83 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.82 (0.29), residues: 833 helix: -4.26 (0.42), residues: 51 sheet: 0.16 (0.29), residues: 334 loop : -0.56 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 47 HIS 0.003 0.001 HIS C 505 PHE 0.021 0.001 PHE G 29 TYR 0.013 0.001 TYR H 91 ARG 0.006 0.000 ARG I 98 Details of bonding type rmsd hydrogen bonds : bond 0.02809 ( 208) hydrogen bonds : angle 5.48241 ( 495) SS BOND : bond 0.00242 ( 12) SS BOND : angle 1.15189 ( 24) covalent geometry : bond 0.00336 ( 6790) covalent geometry : angle 0.52332 ( 9219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: F 100 GLN cc_start: 0.7881 (mp10) cc_final: 0.7659 (mt0) REVERT: G 54 ILE cc_start: 0.9170 (tp) cc_final: 0.8788 (mm) REVERT: H 108 ARG cc_start: 0.5024 (ptt-90) cc_final: 0.4700 (ptt90) REVERT: I 3 GLN cc_start: 0.7761 (pm20) cc_final: 0.7282 (pm20) REVERT: I 35 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9051 (mt) outliers start: 22 outliers final: 15 residues processed: 151 average time/residue: 0.2154 time to fit residues: 42.0064 Evaluate side-chains 152 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 13 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.084266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.071106 restraints weight = 14258.390| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.70 r_work: 0.2834 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6802 Z= 0.143 Angle : 0.526 6.576 9243 Z= 0.277 Chirality : 0.044 0.145 991 Planarity : 0.003 0.031 1184 Dihedral : 4.114 14.277 935 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.46 % Allowed : 14.38 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.84 (0.29), residues: 833 helix: -4.34 (0.40), residues: 51 sheet: 0.16 (0.29), residues: 336 loop : -0.59 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 47 HIS 0.003 0.001 HIS C 505 PHE 0.030 0.001 PHE G 29 TYR 0.013 0.001 TYR H 91 ARG 0.003 0.000 ARG I 87 Details of bonding type rmsd hydrogen bonds : bond 0.02770 ( 208) hydrogen bonds : angle 5.40893 ( 495) SS BOND : bond 0.00271 ( 12) SS BOND : angle 1.03836 ( 24) covalent geometry : bond 0.00335 ( 6790) covalent geometry : angle 0.52444 ( 9219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: F 100 GLN cc_start: 0.7909 (mp10) cc_final: 0.7694 (mt0) REVERT: H 108 ARG cc_start: 0.4876 (ptt-90) cc_final: 0.4661 (ptt90) REVERT: I 3 GLN cc_start: 0.7739 (pm20) cc_final: 0.7251 (pm20) REVERT: I 35 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9049 (mt) outliers start: 25 outliers final: 19 residues processed: 153 average time/residue: 0.2015 time to fit residues: 40.1989 Evaluate side-chains 156 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 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 = 0.3198 r_free = 0.3198 target = 0.085060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.071994 restraints weight = 14028.765| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.68 r_work: 0.2847 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6802 Z= 0.144 Angle : 0.535 7.588 9243 Z= 0.279 Chirality : 0.044 0.146 991 Planarity : 0.003 0.030 1184 Dihedral : 4.106 14.174 935 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.18 % Allowed : 15.21 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.86 (0.29), residues: 833 helix: -4.38 (0.39), residues: 51 sheet: 0.17 (0.29), residues: 336 loop : -0.61 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 47 HIS 0.003 0.001 HIS C 505 PHE 0.029 0.001 PHE G 29 TYR 0.013 0.001 TYR H 91 ARG 0.003 0.000 ARG I 87 Details of bonding type rmsd hydrogen bonds : bond 0.02776 ( 208) hydrogen bonds : angle 5.37359 ( 495) SS BOND : bond 0.00249 ( 12) SS BOND : angle 0.92174 ( 24) covalent geometry : bond 0.00337 ( 6790) covalent geometry : angle 0.53397 ( 9219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: I 3 GLN cc_start: 0.7795 (pm20) cc_final: 0.7301 (pm20) REVERT: I 35 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9050 (mt) outliers start: 23 outliers final: 19 residues processed: 153 average time/residue: 0.2059 time to fit residues: 40.7737 Evaluate side-chains 159 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 15 optimal weight: 0.0050 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.084817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.071984 restraints weight = 14010.840| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.64 r_work: 0.2840 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6802 Z= 0.166 Angle : 0.568 7.115 9243 Z= 0.295 Chirality : 0.045 0.146 991 Planarity : 0.003 0.031 1184 Dihedral : 4.202 14.482 935 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.32 % Allowed : 15.91 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.90 (0.29), residues: 833 helix: -4.39 (0.39), residues: 51 sheet: 0.16 (0.29), residues: 336 loop : -0.67 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 47 HIS 0.003 0.001 HIS C 505 PHE 0.027 0.001 PHE G 29 TYR 0.014 0.001 TYR H 91 ARG 0.010 0.000 ARG I 98 Details of bonding type rmsd hydrogen bonds : bond 0.02900 ( 208) hydrogen bonds : angle 5.42725 ( 495) SS BOND : bond 0.00263 ( 12) SS BOND : angle 0.92581 ( 24) covalent geometry : bond 0.00390 ( 6790) covalent geometry : angle 0.56694 ( 9219) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: F 4 MET cc_start: 0.8532 (mmm) cc_final: 0.7634 (mmm) REVERT: I 3 GLN cc_start: 0.7819 (pm20) cc_final: 0.7335 (pm20) outliers start: 24 outliers final: 20 residues processed: 154 average time/residue: 0.2497 time to fit residues: 50.3629 Evaluate side-chains 159 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3184 r_free = 0.3184 target = 0.084333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.071392 restraints weight = 14074.494| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.65 r_work: 0.2839 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6802 Z= 0.163 Angle : 0.572 9.206 9243 Z= 0.296 Chirality : 0.045 0.146 991 Planarity : 0.003 0.032 1184 Dihedral : 4.223 15.221 935 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.04 % Allowed : 17.29 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.91 (0.29), residues: 833 helix: -4.37 (0.40), residues: 51 sheet: 0.14 (0.29), residues: 336 loop : -0.66 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 47 HIS 0.003 0.001 HIS C 505 PHE 0.028 0.001 PHE G 29 TYR 0.013 0.001 TYR H 91 ARG 0.004 0.000 ARG I 87 Details of bonding type rmsd hydrogen bonds : bond 0.02928 ( 208) hydrogen bonds : angle 5.43316 ( 495) SS BOND : bond 0.00258 ( 12) SS BOND : angle 0.91625 ( 24) covalent geometry : bond 0.00384 ( 6790) covalent geometry : angle 0.57109 ( 9219) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: I 3 GLN cc_start: 0.7827 (pm20) cc_final: 0.7341 (pm20) REVERT: I 35 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9067 (mt) outliers start: 22 outliers final: 18 residues processed: 149 average time/residue: 0.2064 time to fit residues: 40.0619 Evaluate side-chains 157 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 37 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 15 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 74 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.086651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.073626 restraints weight = 14008.869| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.65 r_work: 0.2882 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6802 Z= 0.105 Angle : 0.564 10.962 9243 Z= 0.288 Chirality : 0.044 0.144 991 Planarity : 0.003 0.031 1184 Dihedral : 3.938 13.386 935 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.49 % Allowed : 17.57 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.29), residues: 833 helix: -4.42 (0.41), residues: 45 sheet: 0.23 (0.29), residues: 336 loop : -0.63 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 47 HIS 0.002 0.000 HIS C 505 PHE 0.029 0.001 PHE G 29 TYR 0.015 0.001 TYR H 94 ARG 0.004 0.000 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.02636 ( 208) hydrogen bonds : angle 5.26204 ( 495) SS BOND : bond 0.00290 ( 12) SS BOND : angle 0.75330 ( 24) covalent geometry : bond 0.00250 ( 6790) covalent geometry : angle 0.56335 ( 9219) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: G 69 THR cc_start: 0.8772 (t) cc_final: 0.8532 (t) REVERT: G 74 LYS cc_start: 0.7665 (mmmt) cc_final: 0.7211 (mmtm) REVERT: I 3 GLN cc_start: 0.7777 (pm20) cc_final: 0.7338 (pm20) REVERT: I 35 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9066 (mt) REVERT: I 59 ASN cc_start: 0.8470 (m110) cc_final: 0.8269 (m-40) outliers start: 18 outliers final: 16 residues processed: 156 average time/residue: 0.3196 time to fit residues: 64.7049 Evaluate side-chains 159 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.085189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.072203 restraints weight = 14027.802| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.65 r_work: 0.2859 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6802 Z= 0.144 Angle : 0.592 10.462 9243 Z= 0.303 Chirality : 0.045 0.148 991 Planarity : 0.004 0.032 1184 Dihedral : 4.130 15.798 935 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.63 % Allowed : 17.70 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.30), residues: 833 helix: -4.58 (0.41), residues: 39 sheet: 0.24 (0.29), residues: 336 loop : -0.68 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 47 HIS 0.003 0.001 HIS C 505 PHE 0.029 0.001 PHE G 29 TYR 0.017 0.001 TYR H 94 ARG 0.004 0.000 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.02862 ( 208) hydrogen bonds : angle 5.32757 ( 495) SS BOND : bond 0.00409 ( 12) SS BOND : angle 2.09214 ( 24) covalent geometry : bond 0.00343 ( 6790) covalent geometry : angle 0.58298 ( 9219) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: I 3 GLN cc_start: 0.7803 (pm20) cc_final: 0.7332 (pm20) REVERT: I 35 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9070 (mt) outliers start: 19 outliers final: 17 residues processed: 151 average time/residue: 0.3007 time to fit residues: 59.7128 Evaluate side-chains 157 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 53 optimal weight: 0.0020 chunk 19 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.085234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.072339 restraints weight = 14194.193| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.61 r_work: 0.2860 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6802 Z= 0.148 Angle : 0.588 10.171 9243 Z= 0.302 Chirality : 0.045 0.147 991 Planarity : 0.003 0.032 1184 Dihedral : 4.187 14.712 935 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.77 % Allowed : 17.43 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.81 (0.29), residues: 833 helix: -4.56 (0.42), residues: 39 sheet: 0.25 (0.29), residues: 336 loop : -0.73 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 47 HIS 0.003 0.001 HIS C 505 PHE 0.029 0.001 PHE G 29 TYR 0.014 0.001 TYR F 94 ARG 0.004 0.000 ARG I 87 Details of bonding type rmsd hydrogen bonds : bond 0.02866 ( 208) hydrogen bonds : angle 5.32633 ( 495) SS BOND : bond 0.00279 ( 12) SS BOND : angle 0.98390 ( 24) covalent geometry : bond 0.00354 ( 6790) covalent geometry : angle 0.58626 ( 9219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6162.85 seconds wall clock time: 110 minutes 24.03 seconds (6624.03 seconds total)