Starting phenix.real_space_refine on Mon Jun 24 16:08:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd3_38264/06_2024/8xd3_38264_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd3_38264/06_2024/8xd3_38264.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd3_38264/06_2024/8xd3_38264_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd3_38264/06_2024/8xd3_38264_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd3_38264/06_2024/8xd3_38264_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd3_38264/06_2024/8xd3_38264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd3_38264/06_2024/8xd3_38264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd3_38264/06_2024/8xd3_38264_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xd3_38264/06_2024/8xd3_38264_neut_updated.pdb" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 3 5.49 5 S 14 5.16 5 C 2115 2.51 5 N 568 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A ASP 133": "OD1" <-> "OD2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3342 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3288 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 418, 3277 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 397} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 418, 3277 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 397} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 3338 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 54 Unusual residues: {'NAP': 1} Classifications: {'peptide': 1, 'undetermined': 1, 'water': 11} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1} Unresolved non-hydrogen planarities: 12 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 118 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 118 " occ=0.50 Time building chain proxies: 4.33, per 1000 atoms: 1.30 Number of scatterers: 3342 At special positions: 0 Unit cell: (69.184, 75.952, 71.44, 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 14 16.00 P 3 15.00 O 642 8.00 N 568 7.00 C 2115 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: 1.33 Conformation dependent library (CDL) restraints added in 1.2 seconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 3 sheets defined 49.0% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 6 through 20 removed outlier: 3.770A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.534A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 134 removed outlier: 5.602A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 303 through 308 removed outlier: 4.487A pdb=" N ASP A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASN A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 340 through 360 removed outlier: 3.538A pdb=" N ASN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 390 Processing helix chain 'A' and resid 395 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.624A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.240A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.829A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 162 hydrogen bonds defined for protein. 471 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: 0.91 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1087 1.34 - 1.46: 674 1.46 - 1.57: 1616 1.57 - 1.69: 2 1.69 - 1.81: 27 Bond restraints: 3406 Sorted by residual: bond pdb=" O2B NAP A 500 " pdb=" P2B NAP A 500 " ideal model delta sigma weight residual 1.736 1.566 0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" C4A NAP A 500 " pdb=" N3A NAP A 500 " ideal model delta sigma weight residual 1.332 1.439 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C6A NAP A 500 " pdb=" N6A NAP A 500 " ideal model delta sigma weight residual 1.335 1.434 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" C8A NAP A 500 " pdb=" N7A NAP A 500 " ideal model delta sigma weight residual 1.301 1.398 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C8A NAP A 500 " pdb=" N9A NAP A 500 " ideal model delta sigma weight residual 1.371 1.463 -0.092 2.00e-02 2.50e+03 2.12e+01 ... (remaining 3401 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.50: 107 106.50 - 113.39: 1861 113.39 - 120.29: 1200 120.29 - 127.18: 1410 127.18 - 134.08: 47 Bond angle restraints: 4625 Sorted by residual: angle pdb=" O THR A 302 " pdb=" C THR A 302 " pdb=" N GLU A 303 " ideal model delta sigma weight residual 122.94 116.83 6.11 1.37e+00 5.33e-01 1.99e+01 angle pdb=" O1A NAP A 500 " pdb=" PA NAP A 500 " pdb=" O2A NAP A 500 " ideal model delta sigma weight residual 121.77 109.66 12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O1N NAP A 500 " pdb=" PN NAP A 500 " pdb=" O2N NAP A 500 " ideal model delta sigma weight residual 122.51 110.58 11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CA THR A 302 " pdb=" C THR A 302 " pdb=" N GLU A 303 " ideal model delta sigma weight residual 115.42 121.67 -6.25 1.64e+00 3.72e-01 1.45e+01 angle pdb=" C ASP A 5 " pdb=" N PRO A 6 " pdb=" CA PRO A 6 " ideal model delta sigma weight residual 119.32 123.59 -4.27 1.14e+00 7.69e-01 1.40e+01 ... (remaining 4620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 1788 16.79 - 33.58: 178 33.58 - 50.37: 55 50.37 - 67.15: 27 67.15 - 83.94: 13 Dihedral angle restraints: 2061 sinusoidal: 860 harmonic: 1201 Sorted by residual: dihedral pdb=" CA ASP A 340 " pdb=" CB ASP A 340 " pdb=" CG ASP A 340 " pdb=" OD1 ASP A 340 " ideal model delta sinusoidal sigma weight residual -30.00 -87.65 57.65 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA BARG A 118 " pdb=" CB BARG A 118 " pdb=" CG BARG A 118 " pdb=" CD BARG A 118 " ideal model delta sinusoidal sigma weight residual -180.00 -121.07 -58.93 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N GLN A 19 " pdb=" CA GLN A 19 " pdb=" CB GLN A 19 " pdb=" CG GLN A 19 " ideal model delta sinusoidal sigma weight residual 60.00 117.02 -57.02 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 2058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 413 0.059 - 0.117: 79 0.117 - 0.176: 8 0.176 - 0.235: 1 0.235 - 0.293: 1 Chirality restraints: 502 Sorted by residual: chirality pdb=" C2B NAP A 500 " pdb=" C1B NAP A 500 " pdb=" C3B NAP A 500 " pdb=" O2B NAP A 500 " both_signs ideal model delta sigma weight residual False -2.75 -2.46 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASP A 133 " pdb=" N ASP A 133 " pdb=" C ASP A 133 " pdb=" CB ASP A 133 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA LYS A 391 " pdb=" N LYS A 391 " pdb=" C LYS A 391 " pdb=" CB LYS A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 499 not shown) Planarity restraints: 590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 302 " -0.014 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C THR A 302 " 0.046 2.00e-02 2.50e+03 pdb=" O THR A 302 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 303 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA AARG A 118 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C AARG A 118 " 0.039 2.00e-02 2.50e+03 pdb=" O AARG A 118 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 119 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BARG A 118 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.13e+00 pdb=" C BARG A 118 " 0.039 2.00e-02 2.50e+03 pdb=" O BARG A 118 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 119 " -0.013 2.00e-02 2.50e+03 ... (remaining 587 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1099 2.84 - 3.35: 3205 3.35 - 3.87: 5843 3.87 - 4.38: 6811 4.38 - 4.90: 11455 Nonbonded interactions: 28413 Sorted by model distance: nonbonded pdb=" O ALA A 223 " pdb=" OG1 THR A 227 " model vdw 2.325 2.440 nonbonded pdb=" OG1 THR A 175 " pdb=" OG SER A 351 " model vdw 2.356 2.440 nonbonded pdb=" OE1 GLN A 357 " pdb=" O HOH A 601 " model vdw 2.402 2.440 nonbonded pdb=" OG1 THR A 68 " pdb=" OD1 ASP A 140 " model vdw 2.406 2.440 nonbonded pdb=" NE ARG A 65 " pdb=" O HOH A 602 " model vdw 2.412 2.520 ... (remaining 28408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 3.390 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.070 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 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 : 0.007 0.170 3406 Z= 0.502 Angle : 0.824 12.112 4625 Z= 0.453 Chirality : 0.047 0.293 502 Planarity : 0.005 0.056 590 Dihedral : 17.440 83.942 1295 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.81 % Allowed : 2.05 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.42), residues: 419 helix: 2.22 (0.34), residues: 211 sheet: -0.35 (0.70), residues: 60 loop : -0.61 (0.52), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.001 0.000 HIS A 394 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 225 ARG 0.001 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.371 Fit side-chains REVERT: A 12 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7605 (mtpp) REVERT: A 149 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8441 (p0) REVERT: A 286 GLU cc_start: 0.8346 (mp0) cc_final: 0.7897 (mp0) outliers start: 12 outliers final: 1 residues processed: 76 average time/residue: 1.5482 time to fit residues: 120.3274 Evaluate side-chains 56 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 167 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3406 Z= 0.339 Angle : 0.539 5.734 4625 Z= 0.281 Chirality : 0.046 0.149 502 Planarity : 0.005 0.049 590 Dihedral : 9.746 58.792 512 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.35 % Allowed : 12.90 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.42), residues: 419 helix: 2.24 (0.36), residues: 204 sheet: -0.02 (0.70), residues: 60 loop : -0.36 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.007 0.003 HIS A 267 PHE 0.011 0.002 PHE A 381 TYR 0.013 0.002 TYR A 363 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.392 Fit side-chains REVERT: A 12 LYS cc_start: 0.7897 (mmtp) cc_final: 0.7531 (mtpp) REVERT: A 209 ASP cc_start: 0.7703 (p0) cc_final: 0.7253 (p0) REVERT: A 267 HIS cc_start: 0.7727 (m170) cc_final: 0.7468 (m170) REVERT: A 286 GLU cc_start: 0.8348 (mp0) cc_final: 0.7745 (mp0) outliers start: 7 outliers final: 2 residues processed: 61 average time/residue: 1.4127 time to fit residues: 88.4458 Evaluate side-chains 54 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 240 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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: 0.8536 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3406 Z= 0.132 Angle : 0.445 4.683 4625 Z= 0.233 Chirality : 0.043 0.136 502 Planarity : 0.004 0.046 590 Dihedral : 8.407 59.762 504 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.17 % Allowed : 15.54 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.42), residues: 419 helix: 2.59 (0.35), residues: 204 sheet: 0.10 (0.69), residues: 60 loop : -0.35 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.005 0.001 HIS A 267 PHE 0.007 0.001 PHE A 341 TYR 0.007 0.001 TYR A 225 ARG 0.005 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.382 Fit side-chains REVERT: A 12 LYS cc_start: 0.7778 (mmtp) cc_final: 0.7426 (mmtm) REVERT: A 209 ASP cc_start: 0.7540 (p0) cc_final: 0.7136 (p0) REVERT: A 283 GLU cc_start: 0.6959 (pm20) cc_final: 0.6722 (pm20) REVERT: A 286 GLU cc_start: 0.8373 (mp0) cc_final: 0.8011 (mp0) outliers start: 3 outliers final: 2 residues processed: 58 average time/residue: 1.3084 time to fit residues: 78.0460 Evaluate side-chains 54 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 240 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3406 Z= 0.150 Angle : 0.452 4.603 4625 Z= 0.235 Chirality : 0.043 0.120 502 Planarity : 0.004 0.046 590 Dihedral : 7.835 59.972 504 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.88 % Favored : 96.88 % Rotamer: Outliers : 1.47 % Allowed : 17.01 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.42), residues: 419 helix: 2.56 (0.35), residues: 204 sheet: 0.24 (0.70), residues: 60 loop : -0.28 (0.53), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.009 0.002 HIS A 267 PHE 0.009 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.375 Fit side-chains REVERT: A 12 LYS cc_start: 0.7738 (mmtp) cc_final: 0.7397 (mmtm) REVERT: A 209 ASP cc_start: 0.7485 (p0) cc_final: 0.7084 (p0) REVERT: A 286 GLU cc_start: 0.8364 (mp0) cc_final: 0.7945 (mp0) outliers start: 4 outliers final: 2 residues processed: 56 average time/residue: 1.2722 time to fit residues: 73.3442 Evaluate side-chains 53 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 302 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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: 0.8608 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3406 Z= 0.334 Angle : 0.528 5.556 4625 Z= 0.273 Chirality : 0.046 0.138 502 Planarity : 0.005 0.048 590 Dihedral : 8.015 59.289 504 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.88 % Favored : 96.88 % Rotamer: Outliers : 2.64 % Allowed : 16.13 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.42), residues: 419 helix: 2.13 (0.35), residues: 204 sheet: 0.10 (0.69), residues: 60 loop : -0.41 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.004 0.002 HIS A 388 PHE 0.012 0.002 PHE A 341 TYR 0.012 0.002 TYR A 363 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.388 Fit side-chains REVERT: A 12 LYS cc_start: 0.7781 (mmtp) cc_final: 0.7451 (mmtm) REVERT: A 209 ASP cc_start: 0.7562 (p0) cc_final: 0.7116 (p0) REVERT: A 246 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6243 (mtt90) outliers start: 8 outliers final: 4 residues processed: 55 average time/residue: 1.4317 time to fit residues: 80.7910 Evaluate side-chains 53 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 302 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 0.2980 chunk 18 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3406 Z= 0.130 Angle : 0.452 5.047 4625 Z= 0.234 Chirality : 0.043 0.156 502 Planarity : 0.004 0.047 590 Dihedral : 7.355 59.594 504 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.64 % Favored : 97.12 % Rotamer: Outliers : 1.76 % Allowed : 17.60 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.42), residues: 419 helix: 2.47 (0.35), residues: 204 sheet: 0.01 (0.70), residues: 62 loop : -0.37 (0.53), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.005 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.007 0.001 TYR A 160 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.379 Fit side-chains REVERT: A 12 LYS cc_start: 0.7740 (mmtp) cc_final: 0.7405 (mmtm) REVERT: A 209 ASP cc_start: 0.7467 (p0) cc_final: 0.7037 (p0) outliers start: 5 outliers final: 3 residues processed: 58 average time/residue: 1.2878 time to fit residues: 76.8997 Evaluate side-chains 56 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 249 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.8553 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3406 Z= 0.162 Angle : 0.462 4.660 4625 Z= 0.238 Chirality : 0.043 0.128 502 Planarity : 0.004 0.047 590 Dihedral : 7.230 59.647 504 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.64 % Favored : 97.12 % Rotamer: Outliers : 1.47 % Allowed : 18.18 % Favored : 80.35 % 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: 1.64 (0.42), residues: 419 helix: 2.47 (0.35), residues: 204 sheet: 0.05 (0.70), residues: 62 loop : -0.35 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.005 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.393 Fit side-chains REVERT: A 12 LYS cc_start: 0.7716 (mmtp) cc_final: 0.7393 (mmtm) REVERT: A 209 ASP cc_start: 0.7480 (p0) cc_final: 0.6991 (p0) outliers start: 4 outliers final: 4 residues processed: 56 average time/residue: 1.3139 time to fit residues: 75.6931 Evaluate side-chains 58 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 302 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.8585 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3406 Z= 0.238 Angle : 0.495 5.148 4625 Z= 0.255 Chirality : 0.044 0.130 502 Planarity : 0.004 0.048 590 Dihedral : 7.340 58.347 504 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.88 % Favored : 96.88 % Rotamer: Outliers : 1.76 % Allowed : 18.18 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.42), residues: 419 helix: 2.33 (0.35), residues: 204 sheet: 0.23 (0.70), residues: 60 loop : -0.34 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.005 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.007 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.393 Fit side-chains REVERT: A 12 LYS cc_start: 0.7742 (mmtp) cc_final: 0.7413 (mmtm) REVERT: A 209 ASP cc_start: 0.7492 (p0) cc_final: 0.6955 (p0) REVERT: A 246 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6262 (mtt90) outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 1.4955 time to fit residues: 87.5412 Evaluate side-chains 55 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 249 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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: 0.8574 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3406 Z= 0.202 Angle : 0.484 5.220 4625 Z= 0.250 Chirality : 0.044 0.124 502 Planarity : 0.004 0.048 590 Dihedral : 7.247 59.298 504 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.64 % Favored : 97.12 % Rotamer: Outliers : 1.76 % Allowed : 18.48 % Favored : 79.77 % 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: 1.53 (0.42), residues: 419 helix: 2.37 (0.35), residues: 204 sheet: 0.01 (0.70), residues: 62 loop : -0.38 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.005 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.007 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.395 Fit side-chains REVERT: A 12 LYS cc_start: 0.7740 (mmtp) cc_final: 0.7412 (mmtm) REVERT: A 22 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6849 (t0) REVERT: A 209 ASP cc_start: 0.7458 (p0) cc_final: 0.6928 (p0) REVERT: A 281 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8248 (m-40) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 1.3165 time to fit residues: 76.0100 Evaluate side-chains 59 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 281 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 4 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8531 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3406 Z= 0.128 Angle : 0.454 5.881 4625 Z= 0.235 Chirality : 0.043 0.135 502 Planarity : 0.004 0.048 590 Dihedral : 6.950 58.232 504 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.40 % Favored : 97.36 % Rotamer: Outliers : 1.47 % Allowed : 18.77 % Favored : 79.77 % 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: 1.72 (0.42), residues: 419 helix: 2.59 (0.35), residues: 204 sheet: 0.16 (0.71), residues: 62 loop : -0.43 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 263 HIS 0.005 0.001 HIS A 267 PHE 0.009 0.001 PHE A 341 TYR 0.006 0.001 TYR A 160 ARG 0.007 0.000 ARG A 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.398 Fit side-chains REVERT: A 12 LYS cc_start: 0.7695 (mmtp) cc_final: 0.7379 (mmtm) REVERT: A 22 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6841 (t0) REVERT: A 209 ASP cc_start: 0.7430 (p0) cc_final: 0.6896 (p0) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 1.3548 time to fit residues: 82.1948 Evaluate side-chains 59 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3189 r_free = 0.3189 target = 0.112579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.088178 restraints weight = 12301.994| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.66 r_work: 0.2700 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3406 Z= 0.259 Angle : 0.512 5.707 4625 Z= 0.264 Chirality : 0.045 0.125 502 Planarity : 0.004 0.048 590 Dihedral : 7.224 58.828 504 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.88 % Favored : 96.88 % Rotamer: Outliers : 2.35 % Allowed : 17.89 % Favored : 79.77 % 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: 1.48 (0.42), residues: 419 helix: 2.33 (0.35), residues: 204 sheet: 0.05 (0.70), residues: 62 loop : -0.45 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.005 0.002 HIS A 388 PHE 0.012 0.002 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.008 0.000 ARG A 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1909.45 seconds wall clock time: 34 minutes 24.29 seconds (2064.29 seconds total)