Starting phenix.real_space_refine on Sun Mar 10 19:53:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/03_2024/8el7_28223_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/03_2024/8el7_28223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/03_2024/8el7_28223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/03_2024/8el7_28223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/03_2024/8el7_28223_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el7_28223/03_2024/8el7_28223_updated.pdb" } resolution = 2.8 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= -0.001 sd= 0.198 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 2921 2.51 5 N 802 2.21 5 O 810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 223": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4562 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1134 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 146, 1118 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 5 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 Conformer: "B" Number of residues, atoms: 146, 1118 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 5 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 bond proxies already assigned to first conformer: 1130 Conformer: "C" Number of residues, atoms: 146, 1118 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 5 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 bond proxies already assigned to first conformer: 1130 Chain: "B" Number of atoms: 3428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3428 Classifications: {'peptide': 458, 'water': 5} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 15, 'TRANS': 442, None: 5} Not linked: pdbres="GLU B 494 " pdbres="HOH B 601 " Not linked: pdbres="HOH B 601 " pdbres="HOH B 602 " Not linked: pdbres="HOH B 602 " pdbres="HOH B 603 " Not linked: pdbres="HOH B 603 " pdbres="HOH B 604 " Not linked: pdbres="HOH B 604 " pdbres="HOH B 605 " Chain breaks: 2 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TPO:plan-1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 15, 'GLU:plan': 19, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 171 Time building chain proxies: 4.17, per 1000 atoms: 0.91 Number of scatterers: 4562 At special positions: 0 Unit cell: (54.5344, 80.0974, 110.773, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 810 8.00 N 802 7.00 C 2921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.2 seconds 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 2 sheets defined 58.8% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.676A pdb=" N PHE A 331 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 375 Processing helix chain 'B' and resid 4 through 10 Processing helix chain 'B' and resid 15 through 28 removed outlier: 3.819A pdb=" N GLU B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 55 removed outlier: 3.896A pdb=" N GLU B 40 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASP B 41 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS B 45 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 51 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 55 " --> pdb=" O LYS B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 75 removed outlier: 4.059A pdb=" N ARG B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 95 Processing helix chain 'B' and resid 111 through 127 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'B' and resid 158 through 174 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 188 through 200 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.535A pdb=" N ASN B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 265 removed outlier: 3.513A pdb=" N SER B 250 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N HIS B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 255 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET B 256 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 287 removed outlier: 4.100A pdb=" N ASN B 287 " --> pdb=" O ASN B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 removed outlier: 4.747A pdb=" N ASP B 294 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 295 " --> pdb=" O CYS B 292 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 354 Processing helix chain 'B' and resid 360 through 376 removed outlier: 4.050A pdb=" N THR B 364 " --> pdb=" O ARG B 360 " (cutoff:3.500A) Proline residue: B 365 - end of helix removed outlier: 3.579A pdb=" N ALA B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 388 removed outlier: 3.840A pdb=" N ASP B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 387 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 414 removed outlier: 3.697A pdb=" N MET B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 414 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 432 removed outlier: 3.634A pdb=" N LEU B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.639A pdb=" N TYR B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 455 Processing helix chain 'B' and resid 476 through 484 Proline residue: B 483 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= B, first strand: chain 'A' and resid 229 through 235 removed outlier: 6.857A pdb=" N SER A 272 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N PHE A 232 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 274 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL A 234 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A 276 " --> pdb=" O VAL A 234 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 566 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: 1.07 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 728 1.31 - 1.44: 1153 1.44 - 1.56: 2711 1.56 - 1.68: 2 1.68 - 1.81: 38 Bond restraints: 4632 Sorted by residual: bond pdb=" O3P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.477 0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" C ARG A 375 " pdb=" CA BARG A 375 " ideal model delta sigma weight residual 1.522 1.430 0.091 1.40e-02 5.10e+03 4.26e+01 bond pdb=" C ARG A 375 " pdb=" CA CARG A 375 " ideal model delta sigma weight residual 1.522 1.430 0.091 1.40e-02 5.10e+03 4.26e+01 bond pdb=" O1P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.480 0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" O2P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.481 0.129 2.00e-02 2.50e+03 4.16e+01 ... (remaining 4627 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.88: 123 106.88 - 113.66: 2658 113.66 - 120.44: 1740 120.44 - 127.21: 1735 127.21 - 133.99: 39 Bond angle restraints: 6295 Sorted by residual: angle pdb=" N GLU B 4 " pdb=" CA GLU B 4 " pdb=" C GLU B 4 " ideal model delta sigma weight residual 111.28 115.77 -4.49 1.09e+00 8.42e-01 1.70e+01 angle pdb=" C TRP B 466 " pdb=" N TYR B 467 " pdb=" CA TYR B 467 " ideal model delta sigma weight residual 121.70 114.71 6.99 1.80e+00 3.09e-01 1.51e+01 angle pdb=" CA TRP B 466 " pdb=" C TRP B 466 " pdb=" N TYR B 467 " ideal model delta sigma weight residual 116.02 121.32 -5.30 1.42e+00 4.96e-01 1.39e+01 angle pdb=" N ALA B 15 " pdb=" CA ALA B 15 " pdb=" C ALA B 15 " ideal model delta sigma weight residual 113.38 117.91 -4.53 1.23e+00 6.61e-01 1.35e+01 angle pdb=" N GLY B 13 " pdb=" CA GLY B 13 " pdb=" C GLY B 13 " ideal model delta sigma weight residual 112.73 116.85 -4.12 1.20e+00 6.94e-01 1.18e+01 ... (remaining 6290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 2582 17.32 - 34.64: 188 34.64 - 51.96: 31 51.96 - 69.28: 6 69.28 - 86.60: 5 Dihedral angle restraints: 2812 sinusoidal: 1029 harmonic: 1783 Sorted by residual: dihedral pdb=" CA GLY B 13 " pdb=" C GLY B 13 " pdb=" N GLU B 14 " pdb=" CA GLU B 14 " ideal model delta harmonic sigma weight residual 180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" C TPO B 473 " pdb=" N TPO B 473 " pdb=" CA TPO B 473 " pdb=" CB TPO B 473 " ideal model delta harmonic sigma weight residual -122.60 -113.38 -9.22 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" N TRP B 466 " pdb=" C TRP B 466 " pdb=" CA TRP B 466 " pdb=" CB TRP B 466 " ideal model delta harmonic sigma weight residual 122.80 114.49 8.31 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 2809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 541 0.038 - 0.077: 177 0.077 - 0.115: 39 0.115 - 0.154: 10 0.154 - 0.192: 4 Chirality restraints: 771 Sorted by residual: chirality pdb=" CA ALA B 15 " pdb=" N ALA B 15 " pdb=" C ALA B 15 " pdb=" CB ALA B 15 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.19 2.00e-01 2.50e+01 9.25e-01 chirality pdb=" CA BARG A 375 " pdb=" N ARG A 375 " pdb=" C ARG A 375 " pdb=" CB BARG A 375 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CA CARG A 375 " pdb=" N ARG A 375 " pdb=" C ARG A 375 " pdb=" CB CARG A 375 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 768 not shown) Planarity restraints: 789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 463 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C GLY B 463 " -0.049 2.00e-02 2.50e+03 pdb=" O GLY B 463 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP B 464 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 5 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C ARG B 5 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG B 5 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA B 6 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 478 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C TYR B 478 " 0.020 2.00e-02 2.50e+03 pdb=" O TYR B 478 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS B 479 " -0.007 2.00e-02 2.50e+03 ... (remaining 786 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1224 2.82 - 3.34: 4059 3.34 - 3.86: 6752 3.86 - 4.38: 7778 4.38 - 4.90: 14119 Nonbonded interactions: 33932 Sorted by model distance: nonbonded pdb=" O LEU B 80 " pdb=" OG1 THR B 84 " model vdw 2.295 2.440 nonbonded pdb=" O LEU B 70 " pdb=" OG SER B 74 " model vdw 2.311 2.440 nonbonded pdb=" N GLU B 3 " pdb=" OE1 GLU B 3 " model vdw 2.356 2.520 nonbonded pdb=" O PRO B 399 " pdb=" ND2 ASN B 407 " model vdw 2.374 2.520 nonbonded pdb=" N ASP B 464 " pdb=" OD1 ASP B 464 " model vdw 2.407 2.520 ... (remaining 33927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 3.510 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.580 Find NCS groups from input model: 0.130 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:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.006 0.133 4632 Z= 0.418 Angle : 0.611 7.578 6295 Z= 0.356 Chirality : 0.042 0.192 771 Planarity : 0.004 0.028 789 Dihedral : 13.128 86.604 1644 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.35), residues: 582 helix: 1.64 (0.28), residues: 355 sheet: 0.82 (0.97), residues: 32 loop : -1.30 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 466 HIS 0.003 0.001 HIS B 262 PHE 0.012 0.001 PHE B 163 TYR 0.009 0.001 TYR B 334 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.536 Fit side-chains REVERT: B 181 GLN cc_start: 0.7585 (mt0) cc_final: 0.7336 (mt0) REVERT: B 335 ASN cc_start: 0.7658 (t0) cc_final: 0.7363 (t0) REVERT: B 372 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6962 (mp0) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 1.4648 time to fit residues: 87.9625 Evaluate side-chains 46 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0050 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN B 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4632 Z= 0.218 Angle : 0.521 6.238 6295 Z= 0.264 Chirality : 0.040 0.123 771 Planarity : 0.004 0.029 789 Dihedral : 3.808 14.860 653 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.17 % Allowed : 5.86 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.35), residues: 582 helix: 1.32 (0.28), residues: 355 sheet: 0.53 (0.94), residues: 32 loop : -1.19 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 466 HIS 0.007 0.001 HIS A 343 PHE 0.018 0.002 PHE B 163 TYR 0.007 0.001 TYR B 334 ARG 0.002 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.504 Fit side-chains REVERT: B 150 LYS cc_start: 0.7306 (mtpp) cc_final: 0.7057 (mtmm) REVERT: B 335 ASN cc_start: 0.7780 (t0) cc_final: 0.7400 (t0) REVERT: B 372 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6955 (mp0) outliers start: 10 outliers final: 5 residues processed: 53 average time/residue: 1.4445 time to fit residues: 79.3521 Evaluate side-chains 48 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 0.0050 chunk 53 optimal weight: 0.9980 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4632 Z= 0.184 Angle : 0.471 5.694 6295 Z= 0.241 Chirality : 0.039 0.127 771 Planarity : 0.004 0.029 789 Dihedral : 3.613 12.357 653 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.74 % Allowed : 8.24 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.35), residues: 582 helix: 1.31 (0.28), residues: 353 sheet: 0.49 (0.94), residues: 32 loop : -1.11 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 466 HIS 0.009 0.001 HIS B 491 PHE 0.016 0.001 PHE B 163 TYR 0.007 0.001 TYR B 334 ARG 0.001 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.478 Fit side-chains REVERT: A 333 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.4935 (ptp90) REVERT: B 150 LYS cc_start: 0.7280 (mtpp) cc_final: 0.6890 (mtmm) REVERT: B 335 ASN cc_start: 0.7798 (t0) cc_final: 0.7400 (t0) REVERT: B 372 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6970 (mp0) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 1.6172 time to fit residues: 80.2296 Evaluate side-chains 48 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.0570 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 0.0010 chunk 32 optimal weight: 1.9990 overall best weight: 1.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4632 Z= 0.196 Angle : 0.477 5.448 6295 Z= 0.244 Chirality : 0.039 0.125 771 Planarity : 0.004 0.030 789 Dihedral : 3.637 12.739 653 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.60 % Allowed : 8.68 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.35), residues: 582 helix: 1.22 (0.28), residues: 354 sheet: 0.45 (0.94), residues: 32 loop : -1.07 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 263 HIS 0.009 0.002 HIS B 491 PHE 0.017 0.001 PHE B 163 TYR 0.007 0.001 TYR B 334 ARG 0.001 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.604 Fit side-chains REVERT: A 333 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.4965 (ptp90) REVERT: B 335 ASN cc_start: 0.7859 (t0) cc_final: 0.7413 (t0) REVERT: B 372 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6785 (mp0) outliers start: 12 outliers final: 7 residues processed: 52 average time/residue: 1.4530 time to fit residues: 78.3338 Evaluate side-chains 53 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4632 Z= 0.426 Angle : 0.659 7.184 6295 Z= 0.336 Chirality : 0.046 0.139 771 Planarity : 0.005 0.036 789 Dihedral : 4.203 17.565 653 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.60 % Allowed : 9.76 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.34), residues: 582 helix: 0.69 (0.27), residues: 351 sheet: 0.09 (0.94), residues: 32 loop : -1.24 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 263 HIS 0.015 0.003 HIS A 343 PHE 0.025 0.002 PHE B 163 TYR 0.014 0.002 TYR B 334 ARG 0.002 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.539 Fit side-chains REVERT: A 333 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.5092 (ptp90) REVERT: B 157 ILE cc_start: 0.7876 (mt) cc_final: 0.7640 (mp) REVERT: B 335 ASN cc_start: 0.8000 (t0) cc_final: 0.7515 (t0) REVERT: B 372 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7076 (mp0) outliers start: 12 outliers final: 6 residues processed: 50 average time/residue: 1.5525 time to fit residues: 80.3476 Evaluate side-chains 49 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4632 Z= 0.122 Angle : 0.415 5.344 6295 Z= 0.217 Chirality : 0.037 0.128 771 Planarity : 0.004 0.029 789 Dihedral : 3.566 20.872 653 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.74 % Allowed : 10.85 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.35), residues: 582 helix: 1.28 (0.28), residues: 354 sheet: 0.30 (0.93), residues: 32 loop : -1.18 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 466 HIS 0.009 0.001 HIS B 491 PHE 0.013 0.001 PHE B 163 TYR 0.007 0.001 TYR B 334 ARG 0.001 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.544 Fit side-chains REVERT: A 333 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.4941 (ptp90) REVERT: B 150 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6709 (mtmm) REVERT: B 335 ASN cc_start: 0.7858 (t0) cc_final: 0.7421 (t0) REVERT: B 372 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6818 (mp0) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 1.3830 time to fit residues: 78.8484 Evaluate side-chains 51 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 26 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4632 Z= 0.172 Angle : 0.451 5.268 6295 Z= 0.233 Chirality : 0.039 0.125 771 Planarity : 0.004 0.030 789 Dihedral : 3.579 19.220 653 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.52 % Allowed : 11.71 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.35), residues: 582 helix: 1.30 (0.28), residues: 353 sheet: 0.41 (0.94), residues: 32 loop : -1.11 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 263 HIS 0.010 0.001 HIS B 491 PHE 0.017 0.001 PHE A 232 TYR 0.007 0.001 TYR B 334 ARG 0.001 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.539 Fit side-chains REVERT: A 333 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.4921 (ptp90) REVERT: B 335 ASN cc_start: 0.7870 (t0) cc_final: 0.7421 (t0) REVERT: B 372 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6798 (mp0) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 1.4058 time to fit residues: 75.8655 Evaluate side-chains 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.0020 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4632 Z= 0.119 Angle : 0.401 5.108 6295 Z= 0.208 Chirality : 0.037 0.124 771 Planarity : 0.003 0.029 789 Dihedral : 3.361 21.755 653 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.52 % Allowed : 11.50 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.36), residues: 582 helix: 1.50 (0.28), residues: 356 sheet: 0.43 (0.92), residues: 32 loop : -1.11 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 204 HIS 0.010 0.001 HIS B 491 PHE 0.016 0.001 PHE A 232 TYR 0.006 0.001 TYR B 334 ARG 0.001 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.535 Fit side-chains REVERT: A 333 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.4900 (ptp90) REVERT: B 335 ASN cc_start: 0.7842 (t0) cc_final: 0.7406 (t0) REVERT: B 372 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6615 (mp0) outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 1.3457 time to fit residues: 68.5758 Evaluate side-chains 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.0060 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4632 Z= 0.156 Angle : 0.432 5.070 6295 Z= 0.224 Chirality : 0.038 0.125 771 Planarity : 0.004 0.030 789 Dihedral : 3.471 21.759 653 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.95 % Allowed : 11.06 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.35), residues: 582 helix: 1.49 (0.28), residues: 354 sheet: 0.43 (0.92), residues: 32 loop : -1.11 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 263 HIS 0.009 0.001 HIS B 491 PHE 0.023 0.001 PHE A 232 TYR 0.006 0.001 TYR B 334 ARG 0.001 0.000 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.563 Fit side-chains REVERT: A 333 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.4870 (ptp90) REVERT: B 335 ASN cc_start: 0.7883 (t0) cc_final: 0.7444 (t0) REVERT: B 372 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6648 (mp0) outliers start: 9 outliers final: 6 residues processed: 49 average time/residue: 1.3685 time to fit residues: 69.7106 Evaluate side-chains 50 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.0970 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 0.3980 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 0.2980 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4632 Z= 0.146 Angle : 0.424 5.060 6295 Z= 0.219 Chirality : 0.038 0.125 771 Planarity : 0.004 0.030 789 Dihedral : 3.449 22.831 653 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.39 % Allowed : 10.63 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.36), residues: 582 helix: 1.54 (0.28), residues: 356 sheet: 0.40 (0.91), residues: 32 loop : -1.13 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 263 HIS 0.009 0.001 HIS B 491 PHE 0.022 0.001 PHE A 232 TYR 0.006 0.001 TYR B 334 ARG 0.001 0.000 ARG A 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1164 Ramachandran restraints generated. 582 Oldfield, 0 Emsley, 582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.551 Fit side-chains REVERT: A 333 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.4865 (ptp90) REVERT: B 335 ASN cc_start: 0.7884 (t0) cc_final: 0.7444 (t0) REVERT: B 372 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6600 (mp0) outliers start: 11 outliers final: 8 residues processed: 51 average time/residue: 1.3565 time to fit residues: 71.8938 Evaluate side-chains 52 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 491 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.101047 restraints weight = 23133.650| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 4.03 r_work: 0.2967 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4632 Z= 0.138 Angle : 0.416 5.014 6295 Z= 0.216 Chirality : 0.037 0.125 771 Planarity : 0.004 0.029 789 Dihedral : 3.421 23.800 653 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.17 % Allowed : 10.85 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.36), residues: 582 helix: 1.55 (0.28), residues: 355 sheet: 0.41 (0.91), residues: 32 loop : -1.13 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 263 HIS 0.009 0.001 HIS B 491 PHE 0.022 0.001 PHE A 232 TYR 0.006 0.001 TYR B 334 ARG 0.001 0.000 ARG B 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1892.76 seconds wall clock time: 34 minutes 19.26 seconds (2059.26 seconds total)