Starting phenix.real_space_refine on Fri Dec 8 02:39:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwk_32868/12_2023/7wwk_32868.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwk_32868/12_2023/7wwk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwk_32868/12_2023/7wwk_32868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwk_32868/12_2023/7wwk_32868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwk_32868/12_2023/7wwk_32868.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwk_32868/12_2023/7wwk_32868.pdb" } 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 Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "G ASP 106": "OD1" <-> "OD2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H ASP 82": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 3.90, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.82 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: 1.95 Time building geometry restraints manager: 2.46 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: 99.68 - 106.55: 191 106.55 - 113.41: 3507 113.41 - 120.27: 2458 120.27 - 127.13: 2992 127.13 - 134.00: 71 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 2.440 nonbonded pdb=" O GLY G 26 " pdb=" OH TYR G 32 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR F 36 " pdb=" OE1 GLN F 89 " model vdw 2.267 2.440 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 2.283 2.520 nonbonded pdb=" OH TYR H 36 " pdb=" OE1 GLN H 89 " model vdw 2.355 2.440 ... (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 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: 10.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 27.400 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.320 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.570 ------------------------------------------------------------------------------- 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 6790 Z= 0.283 Angle : 0.711 7.777 9219 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2240 time to fit residues: 45.5045 Evaluate side-chains 142 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0431 ------------------------------------------------------------------------------- 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: 0.0870 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6790 Z= 0.224 Angle : 0.532 7.251 9219 Z= 0.279 Chirality : 0.045 0.136 991 Planarity : 0.003 0.031 1184 Dihedral : 4.123 14.111 935 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.07 % Allowed : 9.96 % Favored : 87.97 % 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: -3.87 (0.45), residues: 57 sheet: 0.17 (0.29), residues: 336 loop : -0.56 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 47 HIS 0.006 0.001 HIS C 505 PHE 0.012 0.001 PHE B 392 TYR 0.015 0.001 TYR H 94 ARG 0.005 0.000 ARG I 87 *********************** 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 154 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 144 average time/residue: 0.2105 time to fit residues: 39.1805 Evaluate side-chains 147 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1044 time to fit residues: 2.7383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 0.0770 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6790 Z= 0.172 Angle : 0.496 7.365 9219 Z= 0.260 Chirality : 0.044 0.139 991 Planarity : 0.003 0.033 1184 Dihedral : 3.962 13.156 935 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.97 % Allowed : 12.59 % Favored : 86.45 % 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: -4.07 (0.42), residues: 57 sheet: 0.17 (0.29), residues: 336 loop : -0.50 (0.30), residues: 440 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 0.007 0.001 PHE B 490 TYR 0.011 0.001 TYR H 91 ARG 0.005 0.000 ARG I 87 *********************** 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 154 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 150 average time/residue: 0.2010 time to fit residues: 39.2582 Evaluate side-chains 138 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0658 time to fit residues: 1.4190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6790 Z= 0.240 Angle : 0.527 7.039 9219 Z= 0.276 Chirality : 0.044 0.143 991 Planarity : 0.003 0.032 1184 Dihedral : 4.161 14.179 935 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.94 % Allowed : 13.69 % Favored : 84.37 % 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: -4.25 (0.42), residues: 51 sheet: 0.14 (0.29), residues: 336 loop : -0.55 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 47 HIS 0.003 0.001 HIS C 505 PHE 0.024 0.001 PHE G 29 TYR 0.014 0.001 TYR H 91 ARG 0.005 0.000 ARG I 87 *********************** 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 150 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 143 average time/residue: 0.2185 time to fit residues: 41.1223 Evaluate side-chains 142 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 0.791 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0653 time to fit residues: 2.1217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 1 optimal weight: 0.0170 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8624 ------------------------------------------------------------------------------- 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** H 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6790 Z= 0.229 Angle : 0.526 6.209 9219 Z= 0.276 Chirality : 0.044 0.143 991 Planarity : 0.003 0.031 1184 Dihedral : 4.144 13.831 935 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.38 % Allowed : 16.74 % Favored : 81.88 % 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: -4.32 (0.43), residues: 45 sheet: 0.13 (0.29), residues: 336 loop : -0.58 (0.30), residues: 452 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 0.032 0.001 PHE G 29 TYR 0.013 0.001 TYR H 91 ARG 0.005 0.000 ARG I 87 *********************** 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 149 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 0.746 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 144 average time/residue: 0.2002 time to fit residues: 37.7360 Evaluate side-chains 140 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0634 time to fit residues: 1.6109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6790 Z= 0.256 Angle : 0.542 6.633 9219 Z= 0.283 Chirality : 0.044 0.145 991 Planarity : 0.003 0.032 1184 Dihedral : 4.211 14.185 935 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.97 % Allowed : 17.70 % Favored : 81.33 % 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: -4.36 (0.43), residues: 45 sheet: 0.12 (0.29), residues: 336 loop : -0.61 (0.30), residues: 452 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 0.014 0.001 TYR H 91 ARG 0.007 0.000 ARG C 355 *********************** 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 145 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 139 average time/residue: 0.2276 time to fit residues: 41.5662 Evaluate side-chains 140 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0721 time to fit residues: 2.0004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6790 Z= 0.229 Angle : 0.545 7.136 9219 Z= 0.283 Chirality : 0.044 0.145 991 Planarity : 0.003 0.032 1184 Dihedral : 4.145 13.761 935 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.28 % Allowed : 19.23 % Favored : 80.50 % 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: -4.36 (0.42), residues: 45 sheet: 0.13 (0.29), residues: 336 loop : -0.61 (0.30), residues: 452 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 0.007 0.000 ARG I 98 *********************** 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 140 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 139 average time/residue: 0.2043 time to fit residues: 37.0048 Evaluate side-chains 137 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.782 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0626 time to fit residues: 1.1408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6790 Z= 0.246 Angle : 0.549 8.538 9219 Z= 0.286 Chirality : 0.044 0.147 991 Planarity : 0.003 0.033 1184 Dihedral : 4.170 14.020 935 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.83 % Allowed : 19.64 % Favored : 79.53 % 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: -4.36 (0.43), residues: 45 sheet: 0.13 (0.29), residues: 336 loop : -0.65 (0.30), residues: 452 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 0.032 0.001 PHE G 29 TYR 0.013 0.001 TYR H 91 ARG 0.006 0.000 ARG I 98 *********************** 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 146 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 0.757 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 142 average time/residue: 0.2115 time to fit residues: 39.0558 Evaluate side-chains 140 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0664 time to fit residues: 1.3313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.0170 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6790 Z= 0.179 Angle : 0.539 9.798 9219 Z= 0.278 Chirality : 0.044 0.145 991 Planarity : 0.003 0.032 1184 Dihedral : 3.966 13.083 935 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 20.47 % Favored : 79.53 % 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: -0.80 (0.29), residues: 833 helix: -4.24 (0.42), residues: 51 sheet: 0.19 (0.29), residues: 336 loop : -0.57 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 47 HIS 0.002 0.000 HIS C 505 PHE 0.033 0.001 PHE G 29 TYR 0.012 0.001 TYR H 94 ARG 0.006 0.000 ARG I 98 *********************** 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 143 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2197 time to fit residues: 40.6334 Evaluate side-chains 138 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 19 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6790 Z= 0.178 Angle : 0.537 10.355 9219 Z= 0.277 Chirality : 0.044 0.147 991 Planarity : 0.003 0.032 1184 Dihedral : 3.962 16.496 935 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.41 % Allowed : 19.92 % 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: -0.78 (0.29), residues: 833 helix: -4.53 (0.39), residues: 45 sheet: 0.24 (0.29), residues: 336 loop : -0.61 (0.30), residues: 452 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 0.033 0.001 PHE G 29 TYR 0.013 0.001 TYR H 94 ARG 0.006 0.000 ARG I 98 ********************** 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 142 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 140 average time/residue: 0.1894 time to fit residues: 34.2810 Evaluate side-chains 140 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1124 time to fit residues: 1.5201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 47 optimal weight: 3.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.086265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.073385 restraints weight = 13915.180| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.58 r_work: 0.2878 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6790 Z= 0.181 Angle : 0.550 10.459 9219 Z= 0.282 Chirality : 0.043 0.146 991 Planarity : 0.003 0.035 1184 Dihedral : 3.929 13.252 935 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 20.33 % 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: -0.78 (0.30), residues: 833 helix: -4.74 (0.36), residues: 39 sheet: 0.17 (0.29), residues: 340 loop : -0.61 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 47 HIS 0.002 0.001 HIS C 505 PHE 0.033 0.001 PHE G 29 TYR 0.013 0.001 TYR H 94 ARG 0.009 0.000 ARG I 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2246.89 seconds wall clock time: 44 minutes 32.32 seconds (2672.32 seconds total)