Starting phenix.real_space_refine on Tue Feb 13 07:24:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnw_27582/02_2024/8dnw_27582.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnw_27582/02_2024/8dnw_27582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnw_27582/02_2024/8dnw_27582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnw_27582/02_2024/8dnw_27582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnw_27582/02_2024/8dnw_27582.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dnw_27582/02_2024/8dnw_27582.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 2689 2.51 5 N 647 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 17": "OD1" <-> "OD2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ASP 389": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4060 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 457 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 251 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "A" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3352 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 416} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 2.93, per 1000 atoms: 0.72 Number of scatterers: 4060 At special positions: 0 Unit cell: (95.55, 79.8, 77.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 698 8.00 N 647 7.00 C 2689 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: 1.80 Conformation dependent library (CDL) restraints added in 731.2 milliseconds 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 3 sheets defined 76.9% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 66 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 69 through 96 removed outlier: 3.644A pdb=" N VAL C 73 " --> pdb=" O GLY C 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 75 through 79 removed outlier: 4.556A pdb=" N LEU A 79 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 98 Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.312A pdb=" N GLY A 135 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 171 removed outlier: 5.999A pdb=" N ALA A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLY A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 197 removed outlier: 3.616A pdb=" N LEU A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'A' and resid 241 through 260 removed outlier: 3.578A pdb=" N LEU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 312 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 383 removed outlier: 3.897A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 408 through 438 removed outlier: 3.557A pdb=" N GLU A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 443 through 467 Processing sheet with id=AA1, first strand: chain 'C' and resid 66 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 282 removed outlier: 3.932A pdb=" N GLY A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 267 " --> pdb=" O GLY A 277 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 924 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: 1.03 Time building geometry restraints manager: 1.94 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: 1231 1.34 - 1.46: 964 1.46 - 1.58: 1908 1.58 - 1.70: 0 1.70 - 1.81: 43 Bond restraints: 4146 Sorted by residual: bond pdb=" CA ILE A 281 " pdb=" CB ILE A 281 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.12e+00 bond pdb=" CG GLU B 32 " pdb=" CD GLU B 32 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.42e-01 bond pdb=" CB GLU B 32 " pdb=" CG GLU B 32 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.79e-01 bond pdb=" CG1 ILE A 48 " pdb=" CD1 ILE A 48 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.71e-01 bond pdb=" CA ILE A 441 " pdb=" CB ILE A 441 " ideal model delta sigma weight residual 1.537 1.528 0.009 1.25e-02 6.40e+03 5.65e-01 ... (remaining 4141 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.80: 116 106.80 - 113.61: 2331 113.61 - 120.41: 1602 120.41 - 127.22: 1531 127.22 - 134.03: 38 Bond angle restraints: 5618 Sorted by residual: angle pdb=" CB MET A 91 " pdb=" CG MET A 91 " pdb=" SD MET A 91 " ideal model delta sigma weight residual 112.70 105.15 7.55 3.00e+00 1.11e-01 6.33e+00 angle pdb=" CB GLU B 32 " pdb=" CG GLU B 32 " pdb=" CD GLU B 32 " ideal model delta sigma weight residual 112.60 116.42 -3.82 1.70e+00 3.46e-01 5.04e+00 angle pdb=" N VAL A 382 " pdb=" CA VAL A 382 " pdb=" C VAL A 382 " ideal model delta sigma weight residual 111.00 113.37 -2.37 1.09e+00 8.42e-01 4.74e+00 angle pdb=" N GLY A 442 " pdb=" CA GLY A 442 " pdb=" C GLY A 442 " ideal model delta sigma weight residual 115.27 112.28 2.99 1.41e+00 5.03e-01 4.49e+00 angle pdb=" C ILE A 90 " pdb=" N MET A 91 " pdb=" CA MET A 91 " ideal model delta sigma weight residual 121.14 117.56 3.58 1.75e+00 3.27e-01 4.18e+00 ... (remaining 5613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.19: 2133 13.19 - 26.37: 217 26.37 - 39.56: 73 39.56 - 52.75: 17 52.75 - 65.93: 3 Dihedral angle restraints: 2443 sinusoidal: 936 harmonic: 1507 Sorted by residual: dihedral pdb=" CA THR A 286 " pdb=" C THR A 286 " pdb=" N SER A 287 " pdb=" CA SER A 287 " ideal model delta harmonic sigma weight residual -180.00 -164.08 -15.92 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ASN A 241 " pdb=" C ASN A 241 " pdb=" N LEU A 242 " pdb=" CA LEU A 242 " ideal model delta harmonic sigma weight residual 180.00 165.48 14.52 0 5.00e+00 4.00e-02 8.43e+00 dihedral pdb=" CB LYS A 392 " pdb=" CG LYS A 392 " pdb=" CD LYS A 392 " pdb=" CE LYS A 392 " ideal model delta sinusoidal sigma weight residual 60.00 105.11 -45.11 3 1.50e+01 4.44e-03 8.11e+00 ... (remaining 2440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 423 0.031 - 0.062: 173 0.062 - 0.092: 56 0.092 - 0.123: 15 0.123 - 0.154: 2 Chirality restraints: 669 Sorted by residual: chirality pdb=" CA MET A 91 " pdb=" N MET A 91 " pdb=" C MET A 91 " pdb=" CB MET A 91 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE A 48 " pdb=" N ILE A 48 " pdb=" C ILE A 48 " pdb=" CB ILE A 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE A 281 " pdb=" N ILE A 281 " pdb=" C ILE A 281 " pdb=" CB ILE A 281 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 666 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 9 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO B 10 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 239 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 240 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 71 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO C 72 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 72 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 72 " 0.021 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 13 2.56 - 3.15: 3351 3.15 - 3.73: 6573 3.73 - 4.32: 8301 4.32 - 4.90: 14462 Nonbonded interactions: 32700 Sorted by model distance: nonbonded pdb=" OE1 GLU A 78 " pdb=" OH TYR A 137 " model vdw 1.976 2.440 nonbonded pdb=" OD2 ASP A 139 " pdb=" OG SER A 141 " model vdw 2.152 2.440 nonbonded pdb=" OG1 THR B 26 " pdb=" OE2 GLU A 264 " model vdw 2.252 2.440 nonbonded pdb=" O VAL A 130 " pdb=" OG1 THR A 134 " model vdw 2.256 2.440 nonbonded pdb=" N THR A 323 " pdb=" O GLY A 339 " model vdw 2.358 2.520 ... (remaining 32695 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 3.620 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.060 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 0.003 0.029 4146 Z= 0.193 Angle : 0.515 7.549 5618 Z= 0.269 Chirality : 0.038 0.154 669 Planarity : 0.004 0.052 687 Dihedral : 12.461 65.934 1475 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 2.85 (0.37), residues: 514 helix: 2.59 (0.26), residues: 384 sheet: -2.76 (1.69), residues: 7 loop : -0.12 (0.61), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.015 0.001 PHE C 85 TYR 0.006 0.001 TYR A 457 ARG 0.002 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.494 Fit side-chains REVERT: B 38 MET cc_start: 0.7454 (tmm) cc_final: 0.6989 (tmm) REVERT: C 76 MET cc_start: 0.7862 (ttp) cc_final: 0.7595 (ttm) REVERT: A 64 TRP cc_start: 0.8316 (m100) cc_final: 0.8110 (m100) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1354 time to fit residues: 11.1996 Evaluate side-chains 53 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.7629 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4146 Z= 0.214 Angle : 0.506 7.256 5618 Z= 0.255 Chirality : 0.038 0.149 669 Planarity : 0.004 0.046 687 Dihedral : 3.534 16.108 557 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.15 % Allowed : 6.22 % Favored : 92.63 % 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: 2.98 (0.37), residues: 514 helix: 2.62 (0.25), residues: 388 sheet: -2.73 (1.65), residues: 7 loop : 0.10 (0.63), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.024 0.001 PHE A 156 TYR 0.008 0.001 TYR A 457 ARG 0.005 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.473 Fit side-chains REVERT: B 38 MET cc_start: 0.7459 (tmm) cc_final: 0.6973 (tmm) REVERT: C 76 MET cc_start: 0.7870 (ttp) cc_final: 0.7614 (ttm) REVERT: C 86 MET cc_start: 0.6848 (mmm) cc_final: 0.6626 (mmm) REVERT: A 149 LEU cc_start: 0.8385 (tt) cc_final: 0.8117 (tt) outliers start: 5 outliers final: 5 residues processed: 55 average time/residue: 0.1347 time to fit residues: 9.9448 Evaluate side-chains 58 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 406 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.0970 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.0000 chunk 16 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.4982 ------------------------------------------------------------------------------- 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: 0.7613 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4146 Z= 0.175 Angle : 0.486 6.898 5618 Z= 0.239 Chirality : 0.037 0.136 669 Planarity : 0.004 0.042 687 Dihedral : 3.464 15.541 557 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.92 % Allowed : 9.45 % Favored : 89.63 % 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: 3.11 (0.37), residues: 514 helix: 2.71 (0.25), residues: 388 sheet: -2.83 (1.61), residues: 7 loop : 0.14 (0.63), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.019 0.001 PHE A 156 TYR 0.005 0.001 TYR A 457 ARG 0.002 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.567 Fit side-chains REVERT: B 38 MET cc_start: 0.7519 (tmm) cc_final: 0.7004 (tmm) REVERT: C 76 MET cc_start: 0.7851 (ttp) cc_final: 0.7616 (ttm) REVERT: C 86 MET cc_start: 0.6846 (mmm) cc_final: 0.6609 (mmm) REVERT: A 149 LEU cc_start: 0.8353 (tt) cc_final: 0.8029 (tt) outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 0.1358 time to fit residues: 10.6049 Evaluate side-chains 55 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 41 optimal weight: 8.9990 chunk 28 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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: 0.7633 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4146 Z= 0.187 Angle : 0.484 6.843 5618 Z= 0.240 Chirality : 0.038 0.137 669 Planarity : 0.004 0.041 687 Dihedral : 3.447 15.582 557 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.69 % Allowed : 10.83 % Favored : 88.48 % 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: 3.06 (0.37), residues: 514 helix: 2.68 (0.25), residues: 388 sheet: -3.22 (1.21), residues: 7 loop : 0.13 (0.63), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 324 HIS 0.002 0.001 HIS B 58 PHE 0.017 0.001 PHE A 156 TYR 0.007 0.001 TYR A 457 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.467 Fit side-chains REVERT: B 38 MET cc_start: 0.7538 (tmm) cc_final: 0.7015 (tmm) REVERT: C 86 MET cc_start: 0.6969 (mmm) cc_final: 0.6726 (mmm) REVERT: A 149 LEU cc_start: 0.8429 (tt) cc_final: 0.8213 (tt) outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.1316 time to fit residues: 9.4835 Evaluate side-chains 53 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7644 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4146 Z= 0.194 Angle : 0.493 7.760 5618 Z= 0.241 Chirality : 0.038 0.136 669 Planarity : 0.004 0.041 687 Dihedral : 3.445 15.992 557 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.15 % Allowed : 12.44 % Favored : 86.41 % 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: 3.13 (0.37), residues: 514 helix: 2.73 (0.25), residues: 388 sheet: -3.19 (1.17), residues: 7 loop : 0.14 (0.63), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.015 0.001 PHE A 156 TYR 0.005 0.001 TYR A 457 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.515 Fit side-chains REVERT: B 38 MET cc_start: 0.7542 (tmm) cc_final: 0.7022 (tmm) REVERT: C 86 MET cc_start: 0.7050 (mmm) cc_final: 0.6820 (mmm) REVERT: A 149 LEU cc_start: 0.8443 (tt) cc_final: 0.8220 (tt) outliers start: 5 outliers final: 2 residues processed: 57 average time/residue: 0.1369 time to fit residues: 10.4927 Evaluate side-chains 57 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.0870 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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: 0.7645 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4146 Z= 0.191 Angle : 0.494 8.647 5618 Z= 0.241 Chirality : 0.037 0.143 669 Planarity : 0.004 0.041 687 Dihedral : 3.427 16.032 557 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.38 % Allowed : 13.59 % Favored : 85.02 % 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: 3.19 (0.38), residues: 514 helix: 2.77 (0.25), residues: 388 sheet: -2.95 (1.25), residues: 7 loop : 0.17 (0.63), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.014 0.001 PHE A 156 TYR 0.006 0.001 TYR A 457 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.483 Fit side-chains REVERT: B 38 MET cc_start: 0.7507 (tmm) cc_final: 0.6991 (tmm) REVERT: A 149 LEU cc_start: 0.8450 (tt) cc_final: 0.8219 (tt) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 0.1273 time to fit residues: 10.0835 Evaluate side-chains 59 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 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: 0.7641 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 : 0.003 0.025 4146 Z= 0.182 Angle : 0.510 9.890 5618 Z= 0.245 Chirality : 0.037 0.155 669 Planarity : 0.004 0.041 687 Dihedral : 3.422 15.861 557 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.38 % Allowed : 14.06 % Favored : 84.56 % 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: 3.25 (0.38), residues: 514 helix: 2.80 (0.25), residues: 388 sheet: -2.55 (1.48), residues: 7 loop : 0.23 (0.64), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.014 0.001 PHE A 156 TYR 0.006 0.001 TYR A 457 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.514 Fit side-chains REVERT: B 38 MET cc_start: 0.7548 (tmm) cc_final: 0.7020 (tmm) REVERT: A 149 LEU cc_start: 0.8428 (tt) cc_final: 0.8199 (tt) outliers start: 6 outliers final: 4 residues processed: 57 average time/residue: 0.1316 time to fit residues: 10.1870 Evaluate side-chains 58 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4146 Z= 0.211 Angle : 0.524 9.949 5618 Z= 0.252 Chirality : 0.038 0.176 669 Planarity : 0.004 0.041 687 Dihedral : 3.464 16.474 557 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.61 % Allowed : 14.52 % Favored : 83.87 % 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: 3.22 (0.38), residues: 514 helix: 2.76 (0.25), residues: 388 sheet: -2.62 (1.53), residues: 7 loop : 0.29 (0.64), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.013 0.001 PHE A 156 TYR 0.006 0.001 TYR A 457 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.479 Fit side-chains REVERT: B 38 MET cc_start: 0.7555 (tmm) cc_final: 0.7030 (tmm) outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.1287 time to fit residues: 9.9466 Evaluate side-chains 59 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.0470 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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: 0.7636 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4146 Z= 0.175 Angle : 0.529 11.493 5618 Z= 0.250 Chirality : 0.038 0.187 669 Planarity : 0.004 0.040 687 Dihedral : 3.432 15.865 557 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.15 % Allowed : 15.21 % Favored : 83.64 % 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: 3.30 (0.38), residues: 514 helix: 2.82 (0.25), residues: 388 sheet: -2.86 (1.46), residues: 7 loop : 0.33 (0.64), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.013 0.001 PHE A 156 TYR 0.006 0.001 TYR A 457 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.491 Fit side-chains REVERT: B 38 MET cc_start: 0.7547 (tmm) cc_final: 0.7026 (tmm) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.1347 time to fit residues: 10.2253 Evaluate side-chains 58 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 12 optimal weight: 0.0770 chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 0.0170 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.3376 ------------------------------------------------------------------------------- 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: 0.7611 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4146 Z= 0.150 Angle : 0.530 13.799 5618 Z= 0.246 Chirality : 0.038 0.218 669 Planarity : 0.004 0.039 687 Dihedral : 3.401 14.595 557 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.38 % Allowed : 14.75 % Favored : 83.87 % 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: 3.37 (0.38), residues: 514 helix: 2.87 (0.25), residues: 388 sheet: -3.05 (1.49), residues: 7 loop : 0.37 (0.64), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.001 0.000 HIS B 58 PHE 0.013 0.001 PHE A 156 TYR 0.005 0.001 TYR A 457 ARG 0.004 0.000 ARG B 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.464 Fit side-chains REVERT: B 38 MET cc_start: 0.7540 (tmm) cc_final: 0.7015 (tmm) outliers start: 6 outliers final: 5 residues processed: 58 average time/residue: 0.1322 time to fit residues: 10.3882 Evaluate side-chains 56 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 27 optimal weight: 0.0670 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.150339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122121 restraints weight = 5315.661| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.90 r_work: 0.3148 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4146 Z= 0.188 Angle : 0.548 13.524 5618 Z= 0.258 Chirality : 0.039 0.202 669 Planarity : 0.004 0.039 687 Dihedral : 3.439 15.118 557 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.15 % Allowed : 15.90 % Favored : 82.95 % 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: 3.26 (0.37), residues: 514 helix: 2.79 (0.25), residues: 388 sheet: -3.14 (1.49), residues: 7 loop : 0.35 (0.64), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 324 HIS 0.002 0.001 HIS B 58 PHE 0.013 0.001 PHE A 156 TYR 0.007 0.001 TYR A 457 ARG 0.003 0.000 ARG B 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1235.14 seconds wall clock time: 22 minutes 48.84 seconds (1368.84 seconds total)