Starting phenix.real_space_refine on Fri Dec 27 10:12:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnw_27582/12_2024/8dnw_27582.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnw_27582/12_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/cci-nas-00/data/ceres_data/8dnw_27582/12_2024/8dnw_27582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnw_27582/12_2024/8dnw_27582.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnw_27582/12_2024/8dnw_27582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnw_27582/12_2024/8dnw_27582.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.033 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. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 3.22, per 1000 atoms: 0.79 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 737.2 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: 0.36 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: 1.18 Time building geometry restraints manager: 1.15 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: 0.00 - 1.51: 5514 1.51 - 3.02: 80 3.02 - 4.53: 17 4.53 - 6.04: 6 6.04 - 7.55: 1 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 3.040 nonbonded pdb=" OD2 ASP A 139 " pdb=" OG SER A 141 " model vdw 2.152 3.040 nonbonded pdb=" OG1 THR B 26 " pdb=" OE2 GLU A 264 " model vdw 2.252 3.040 nonbonded pdb=" O VAL A 130 " pdb=" OG1 THR A 134 " model vdw 2.256 3.040 nonbonded pdb=" N THR A 323 " pdb=" O GLY A 339 " model vdw 2.358 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.680 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.150 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.417 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: 0.1420 time to fit residues: 11.6541 Evaluate side-chains 53 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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: 0.6980 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 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: 0.0820 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= 0.215 Angle : 0.512 7.240 5618 Z= 0.260 Chirality : 0.039 0.152 669 Planarity : 0.004 0.046 687 Dihedral : 3.620 15.756 557 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.15 % Allowed : 6.45 % Favored : 92.40 % 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: 2.93 (0.37), residues: 514 helix: 2.59 (0.25), residues: 388 sheet: -2.75 (1.65), residues: 7 loop : 0.04 (0.62), 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 0.023 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 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.477 Fit side-chains REVERT: B 38 MET cc_start: 0.7456 (tmm) cc_final: 0.6969 (tmm) REVERT: C 76 MET cc_start: 0.7876 (ttp) cc_final: 0.7608 (ttm) REVERT: C 86 MET cc_start: 0.6848 (mmm) cc_final: 0.6627 (mmm) REVERT: A 149 LEU cc_start: 0.8386 (tt) cc_final: 0.8060 (tt) outliers start: 5 outliers final: 4 residues processed: 60 average time/residue: 0.1320 time to fit residues: 10.6773 Evaluate side-chains 59 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL 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: 2.9990 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 46 optimal weight: 0.0370 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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: 0.7610 moved from start: 0.1066 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= 0.168 Angle : 0.482 6.843 5618 Z= 0.241 Chirality : 0.038 0.135 669 Planarity : 0.004 0.042 687 Dihedral : 3.538 14.925 557 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.15 % Allowed : 8.76 % Favored : 90.09 % 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: 3.05 (0.37), residues: 514 helix: 2.69 (0.25), residues: 388 sheet: -2.82 (1.62), residues: 7 loop : 0.04 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 324 HIS 0.001 0.001 HIS B 58 PHE 0.019 0.001 PHE A 156 TYR 0.006 0.001 TYR A 137 ARG 0.003 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 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.459 Fit side-chains REVERT: B 38 MET cc_start: 0.7524 (tmm) cc_final: 0.7001 (tmm) REVERT: C 86 MET cc_start: 0.6846 (mmm) cc_final: 0.6604 (mmm) REVERT: A 149 LEU cc_start: 0.8402 (tt) cc_final: 0.8075 (tt) REVERT: A 153 ILE cc_start: 0.8676 (mm) cc_final: 0.8458 (mm) outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.1289 time to fit residues: 10.4785 Evaluate side-chains 59 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 400 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.0670 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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: 0.1267 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= 0.190 Angle : 0.488 6.940 5618 Z= 0.242 Chirality : 0.038 0.138 669 Planarity : 0.004 0.040 687 Dihedral : 3.501 15.291 557 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.15 % Allowed : 10.60 % Favored : 88.25 % 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: 3.03 (0.37), residues: 514 helix: 2.66 (0.25), residues: 388 sheet: -2.92 (1.44), residues: 7 loop : 0.10 (0.62), 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 0.016 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 62 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.474 Fit side-chains REVERT: B 38 MET cc_start: 0.7540 (tmm) cc_final: 0.7013 (tmm) REVERT: C 86 MET cc_start: 0.6961 (mmm) cc_final: 0.6729 (mmm) REVERT: A 149 LEU cc_start: 0.8398 (tt) cc_final: 0.8171 (tt) REVERT: A 153 ILE cc_start: 0.8655 (mm) cc_final: 0.8431 (mm) outliers start: 5 outliers final: 3 residues processed: 58 average time/residue: 0.1271 time to fit residues: 10.0748 Evaluate side-chains 62 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 400 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 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: 0.7630 moved from start: 0.1352 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= 0.182 Angle : 0.487 7.422 5618 Z= 0.240 Chirality : 0.038 0.135 669 Planarity : 0.004 0.040 687 Dihedral : 3.485 15.318 557 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.61 % Allowed : 12.44 % Favored : 85.94 % 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: 3.14 (0.37), residues: 514 helix: 2.73 (0.25), residues: 388 sheet: -2.93 (1.30), 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 0.015 0.001 PHE A 156 TYR 0.006 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 67 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.471 Fit side-chains REVERT: B 38 MET cc_start: 0.7535 (tmm) cc_final: 0.7019 (tmm) REVERT: C 86 MET cc_start: 0.7064 (mmm) cc_final: 0.6835 (mmm) REVERT: A 149 LEU cc_start: 0.8397 (tt) cc_final: 0.8150 (tt) REVERT: A 153 ILE cc_start: 0.8656 (mm) cc_final: 0.8418 (mm) outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 0.1234 time to fit residues: 10.5249 Evaluate side-chains 63 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7661 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4146 Z= 0.223 Angle : 0.508 8.401 5618 Z= 0.250 Chirality : 0.038 0.149 669 Planarity : 0.004 0.041 687 Dihedral : 3.516 16.193 557 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.84 % Allowed : 13.36 % Favored : 84.79 % 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: 3.12 (0.37), residues: 514 helix: 2.70 (0.25), residues: 388 sheet: -2.73 (1.40), residues: 7 loop : 0.20 (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 0.014 0.001 PHE A 156 TYR 0.008 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 66 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.501 Fit side-chains REVERT: B 38 MET cc_start: 0.7574 (tmm) cc_final: 0.7031 (tmm) REVERT: A 149 LEU cc_start: 0.8435 (tt) cc_final: 0.8182 (tt) REVERT: A 153 ILE cc_start: 0.8712 (mm) cc_final: 0.8483 (mm) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.1247 time to fit residues: 10.6018 Evaluate side-chains 63 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 152 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 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: 0.7653 moved from start: 0.1539 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= 0.198 Angle : 0.509 9.843 5618 Z= 0.248 Chirality : 0.038 0.150 669 Planarity : 0.004 0.040 687 Dihedral : 3.509 16.156 557 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.84 % Allowed : 14.52 % 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: 3.13 (0.37), residues: 514 helix: 2.70 (0.25), residues: 388 sheet: -2.61 (1.47), residues: 7 loop : 0.23 (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 0.013 0.001 PHE A 156 TYR 0.007 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 66 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.480 Fit side-chains REVERT: B 38 MET cc_start: 0.7558 (tmm) cc_final: 0.7025 (tmm) REVERT: A 149 LEU cc_start: 0.8411 (tt) cc_final: 0.8160 (tt) REVERT: A 153 ILE cc_start: 0.8681 (mm) cc_final: 0.8435 (mm) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.1313 time to fit residues: 11.3620 Evaluate side-chains 65 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 152 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1575 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= 0.210 Angle : 0.516 10.361 5618 Z= 0.251 Chirality : 0.038 0.166 669 Planarity : 0.004 0.041 687 Dihedral : 3.532 16.160 557 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.84 % Allowed : 14.98 % Favored : 83.18 % 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: 3.12 (0.37), residues: 514 helix: 2.68 (0.25), residues: 388 sheet: -2.78 (1.48), residues: 7 loop : 0.29 (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 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 68 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.486 Fit side-chains REVERT: B 38 MET cc_start: 0.7555 (tmm) cc_final: 0.7030 (tmm) REVERT: A 149 LEU cc_start: 0.8416 (tt) cc_final: 0.8153 (tt) REVERT: A 153 ILE cc_start: 0.8687 (mm) cc_final: 0.8450 (mm) outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 0.1227 time to fit residues: 10.7478 Evaluate side-chains 66 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 152 THR 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: 0.5980 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 0.0670 chunk 51 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1655 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= 0.166 Angle : 0.529 11.976 5618 Z= 0.252 Chirality : 0.038 0.181 669 Planarity : 0.004 0.040 687 Dihedral : 3.528 15.296 557 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.69 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: 3.20 (0.37), residues: 514 helix: 2.74 (0.25), residues: 388 sheet: -3.07 (1.47), residues: 7 loop : 0.34 (0.64), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 324 HIS 0.001 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 *********************** 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 63 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.544 Fit side-chains REVERT: B 38 MET cc_start: 0.7546 (tmm) cc_final: 0.7024 (tmm) REVERT: A 149 LEU cc_start: 0.8365 (tt) cc_final: 0.8119 (tt) REVERT: A 153 ILE cc_start: 0.8677 (mm) cc_final: 0.8429 (mm) outliers start: 5 outliers final: 4 residues processed: 60 average time/residue: 0.1296 time to fit residues: 10.6802 Evaluate side-chains 60 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 0.0670 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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: 0.1684 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= 0.189 Angle : 0.529 11.357 5618 Z= 0.253 Chirality : 0.038 0.175 669 Planarity : 0.004 0.040 687 Dihedral : 3.510 15.731 557 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.38 % Allowed : 15.90 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.37), residues: 514 helix: 2.72 (0.25), residues: 388 sheet: -3.17 (1.48), residues: 7 loop : 0.41 (0.64), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 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 ********************** 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 62 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.482 Fit side-chains REVERT: B 38 MET cc_start: 0.7558 (tmm) cc_final: 0.7040 (tmm) REVERT: A 149 LEU cc_start: 0.8397 (tt) cc_final: 0.8147 (tt) REVERT: A 153 ILE cc_start: 0.8643 (mm) cc_final: 0.8399 (mm) outliers start: 6 outliers final: 5 residues processed: 58 average time/residue: 0.1324 time to fit residues: 10.3953 Evaluate side-chains 60 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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: 1.9990 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.150870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122576 restraints weight = 5303.360| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.89 r_work: 0.3164 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1707 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= 0.192 Angle : 0.543 11.316 5618 Z= 0.259 Chirality : 0.038 0.170 669 Planarity : 0.004 0.040 687 Dihedral : 3.521 15.763 557 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.15 % Allowed : 16.36 % Favored : 82.49 % 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 (0.37), residues: 514 helix: 2.71 (0.25), residues: 388 sheet: -3.17 (1.50), residues: 7 loop : 0.45 (0.64), 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 0.013 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: 1162.17 seconds wall clock time: 21 minutes 46.58 seconds (1306.58 seconds total)