Starting phenix.real_space_refine on Fri Dec 27 10:43:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8do3_27589/12_2024/8do3_27589_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8do3_27589/12_2024/8do3_27589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8do3_27589/12_2024/8do3_27589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8do3_27589/12_2024/8do3_27589.map" model { file = "/net/cci-nas-00/data/ceres_data/8do3_27589/12_2024/8do3_27589_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8do3_27589/12_2024/8do3_27589_trim.cif" } resolution = 3.22 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= 0.004 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 26 5.16 5 Cl 2 4.86 5 C 2765 2.51 5 N 676 2.21 5 O 716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4185 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "A" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3431 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'SWR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.22, per 1000 atoms: 0.77 Number of scatterers: 4185 At special positions: 0 Unit cell: (86.1, 76.65, 81.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 26 16.00 O 716 8.00 N 676 7.00 C 2765 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: 1.10 Conformation dependent library (CDL) restraints added in 521.5 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 76.6% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.560A pdb=" N SER B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 66 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 69 through 95 Processing helix chain 'A' and resid 8 through 14 removed outlier: 4.257A pdb=" N PHE A 12 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 75 through 79 removed outlier: 4.600A pdb=" N LEU A 79 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 107 through 134 Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.789A pdb=" N GLY A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 172 Processing helix chain 'A' and resid 177 through 197 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 Processing helix chain 'A' and resid 288 through 312 Processing helix chain 'A' and resid 315 through 322 Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 384 removed outlier: 4.018A pdb=" N GLY A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 405 through 408 Processing helix chain 'A' and resid 409 through 415 Processing helix chain 'A' and resid 416 through 439 Processing helix chain 'A' and resid 442 through 468 removed outlier: 3.539A pdb=" N GLY A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 202 Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 282 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 325 removed outlier: 3.632A pdb=" N GLY A 339 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N SER A 325 " --> pdb=" O PRO A 337 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 942 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: 1.05 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1056 1.33 - 1.45: 765 1.45 - 1.57: 2409 1.57 - 1.69: 1 1.69 - 1.81: 45 Bond restraints: 4276 Sorted by residual: bond pdb=" C2 SWR A 501 " pdb=" N5 SWR A 501 " ideal model delta sigma weight residual 1.463 1.526 -0.063 2.00e-02 2.50e+03 9.91e+00 bond pdb=" C6 SWR A 501 " pdb=" C7 SWR A 501 " ideal model delta sigma weight residual 1.433 1.395 0.038 2.00e-02 2.50e+03 3.68e+00 bond pdb=" CA ALA A 440 " pdb=" C ALA A 440 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.30e-02 5.92e+03 2.60e+00 bond pdb=" CA THR A 445 " pdb=" C THR A 445 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.24e-02 6.50e+03 2.55e+00 bond pdb=" CA TYR A 63 " pdb=" C TYR A 63 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.38e-02 5.25e+03 2.51e+00 ... (remaining 4271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 5631 1.60 - 3.20: 118 3.20 - 4.79: 32 4.79 - 6.39: 7 6.39 - 7.99: 2 Bond angle restraints: 5790 Sorted by residual: angle pdb=" N ILE A 441 " pdb=" CA ILE A 441 " pdb=" C ILE A 441 " ideal model delta sigma weight residual 109.58 105.73 3.85 1.29e+00 6.01e-01 8.91e+00 angle pdb=" N SWR A 501 " pdb=" C2 SWR A 501 " pdb=" N5 SWR A 501 " ideal model delta sigma weight residual 110.48 118.47 -7.99 3.00e+00 1.11e-01 7.10e+00 angle pdb=" C19 SWR A 501 " pdb=" N5 SWR A 501 " pdb=" C2 SWR A 501 " ideal model delta sigma weight residual 125.55 117.82 7.73 3.00e+00 1.11e-01 6.65e+00 angle pdb=" C LYS A 171 " pdb=" N GLY A 172 " pdb=" CA GLY A 172 " ideal model delta sigma weight residual 121.41 117.18 4.23 1.96e+00 2.60e-01 4.65e+00 angle pdb=" C25 SWR A 501 " pdb=" C20 SWR A 501 " pdb=" N6 SWR A 501 " ideal model delta sigma weight residual 123.71 117.45 6.26 3.00e+00 1.11e-01 4.35e+00 ... (remaining 5785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 2282 16.42 - 32.84: 204 32.84 - 49.26: 31 49.26 - 65.68: 11 65.68 - 82.10: 4 Dihedral angle restraints: 2532 sinusoidal: 1008 harmonic: 1524 Sorted by residual: dihedral pdb=" CA ASN A 300 " pdb=" CB ASN A 300 " pdb=" CG ASN A 300 " pdb=" OD1 ASN A 300 " ideal model delta sinusoidal sigma weight residual 120.00 -173.50 -66.50 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA ILE A 401 " pdb=" C ILE A 401 " pdb=" N ASN A 402 " pdb=" CA ASN A 402 " ideal model delta harmonic sigma weight residual -180.00 -164.96 -15.04 0 5.00e+00 4.00e-02 9.05e+00 dihedral pdb=" CB GLU A 264 " pdb=" CG GLU A 264 " pdb=" CD GLU A 264 " pdb=" OE1 GLU A 264 " ideal model delta sinusoidal sigma weight residual 0.00 -80.48 80.48 1 3.00e+01 1.11e-03 8.90e+00 ... (remaining 2529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 421 0.031 - 0.061: 175 0.061 - 0.092: 64 0.092 - 0.123: 14 0.123 - 0.154: 3 Chirality restraints: 677 Sorted by residual: chirality pdb=" CA ILE A 441 " pdb=" N ILE A 441 " pdb=" C ILE A 441 " pdb=" CB ILE A 441 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" C2 SWR A 501 " pdb=" N SWR A 501 " pdb=" C1 SWR A 501 " pdb=" N5 SWR A 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.60 0.14 2.00e-01 2.50e+01 4.74e-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 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 674 not shown) Planarity restraints: 709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 SWR A 501 " 0.205 2.00e-02 2.50e+03 6.09e-01 6.49e+03 pdb=" C2 SWR A 501 " 0.224 2.00e-02 2.50e+03 pdb=" C20 SWR A 501 " -0.290 2.00e-02 2.50e+03 pdb=" N5 SWR A 501 " -0.354 2.00e-02 2.50e+03 pdb=" N6 SWR A 501 " -0.481 2.00e-02 2.50e+03 pdb=" O5 SWR A 501 " 1.302 2.00e-02 2.50e+03 pdb=" O6 SWR A 501 " -0.605 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N SWR A 501 " 0.059 2.00e-02 2.50e+03 2.13e-01 9.11e+02 pdb=" O SWR A 501 " -0.212 2.00e-02 2.50e+03 pdb=" C1 SWR A 501 " -0.381 2.00e-02 2.50e+03 pdb=" C13 SWR A 501 " 0.117 2.00e-02 2.50e+03 pdb=" C2 SWR A 501 " 0.190 2.00e-02 2.50e+03 pdb=" C3 SWR A 501 " -0.079 2.00e-02 2.50e+03 pdb=" C4 SWR A 501 " 0.338 2.00e-02 2.50e+03 pdb=" N1 SWR A 501 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 SWR A 501 " -0.027 2.00e-02 2.50e+03 5.54e-02 6.14e+01 pdb=" C21 SWR A 501 " -0.038 2.00e-02 2.50e+03 pdb=" C22 SWR A 501 " -0.032 2.00e-02 2.50e+03 pdb=" C23 SWR A 501 " -0.015 2.00e-02 2.50e+03 pdb=" C24 SWR A 501 " -0.034 2.00e-02 2.50e+03 pdb=" C25 SWR A 501 " -0.043 2.00e-02 2.50e+03 pdb=" N6 SWR A 501 " 0.104 2.00e-02 2.50e+03 pdb="CL1 SWR A 501 " 0.085 2.00e-02 2.50e+03 ... (remaining 706 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 1840 2.94 - 3.43: 4518 3.43 - 3.92: 7024 3.92 - 4.41: 7554 4.41 - 4.90: 13088 Nonbonded interactions: 34024 Sorted by model distance: nonbonded pdb=" O THR A 124 " pdb=" OG SER A 128 " model vdw 2.452 3.040 nonbonded pdb=" O LEU A 181 " pdb=" OG1 THR A 185 " model vdw 2.461 3.040 nonbonded pdb=" O GLN A 20 " pdb=" OH TYR A 173 " model vdw 2.464 3.040 nonbonded pdb=" NH2 ARG B 20 " pdb=" O LYS A 415 " model vdw 2.523 3.120 nonbonded pdb=" O VAL B 8 " pdb=" OG SER B 11 " model vdw 2.538 3.040 ... (remaining 34019 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.120 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 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 : 0.004 0.063 4276 Z= 0.281 Angle : 0.621 7.992 5790 Z= 0.313 Chirality : 0.039 0.154 677 Planarity : 0.025 0.609 709 Dihedral : 13.224 82.100 1554 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 2.39 (0.37), residues: 522 helix: 2.48 (0.26), residues: 393 sheet: -1.48 (1.46), residues: 14 loop : -1.34 (0.52), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.011 0.001 PHE A 252 TYR 0.006 0.001 TYR A 131 ARG 0.005 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.806 Fit side-chains REVERT: B 30 ARG cc_start: 0.7320 (tpp80) cc_final: 0.6345 (mmm160) REVERT: A 82 SER cc_start: 0.8718 (t) cc_final: 0.8456 (t) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2340 time to fit residues: 17.0266 Evaluate side-chains 53 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.7537 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4276 Z= 0.248 Angle : 0.564 6.014 5790 Z= 0.278 Chirality : 0.039 0.128 677 Planarity : 0.004 0.039 709 Dihedral : 5.155 31.642 594 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.12 % Allowed : 4.24 % Favored : 94.64 % 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: 2.63 (0.37), residues: 522 helix: 2.57 (0.26), residues: 396 sheet: -1.66 (1.45), residues: 14 loop : -0.97 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.008 0.001 PHE A 252 TYR 0.007 0.001 TYR A 63 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.471 Fit side-chains REVERT: B 30 ARG cc_start: 0.7463 (tpp80) cc_final: 0.6490 (mmm160) REVERT: B 55 LYS cc_start: 0.8308 (tttt) cc_final: 0.7956 (tttp) REVERT: A 24 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5241 (mmt180) REVERT: A 82 SER cc_start: 0.8785 (t) cc_final: 0.8549 (t) outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 0.2284 time to fit residues: 16.1061 Evaluate side-chains 59 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 463 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.0270 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 0.0570 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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: 0.7512 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4276 Z= 0.186 Angle : 0.516 6.051 5790 Z= 0.256 Chirality : 0.037 0.127 677 Planarity : 0.004 0.038 709 Dihedral : 4.960 27.728 594 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.89 % Allowed : 7.14 % Favored : 91.96 % 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: 2.77 (0.37), residues: 522 helix: 2.65 (0.26), residues: 396 sheet: -1.81 (1.33), residues: 14 loop : -0.80 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.001 0.001 HIS A 218 PHE 0.007 0.001 PHE A 156 TYR 0.006 0.001 TYR A 137 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.590 Fit side-chains REVERT: B 30 ARG cc_start: 0.7462 (tpp80) cc_final: 0.6428 (mmm160) REVERT: A 24 ARG cc_start: 0.6292 (OUTLIER) cc_final: 0.5241 (mmt180) REVERT: A 77 MET cc_start: 0.8380 (mmt) cc_final: 0.8019 (mmt) REVERT: A 82 SER cc_start: 0.8834 (t) cc_final: 0.8559 (t) outliers start: 4 outliers final: 1 residues processed: 54 average time/residue: 0.2109 time to fit residues: 13.8937 Evaluate side-chains 51 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 163 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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: 0.7518 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4276 Z= 0.200 Angle : 0.522 6.146 5790 Z= 0.257 Chirality : 0.038 0.128 677 Planarity : 0.004 0.039 709 Dihedral : 5.076 29.230 594 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.34 % Allowed : 8.48 % Favored : 90.18 % 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: 2.81 (0.37), residues: 522 helix: 2.68 (0.26), residues: 396 sheet: -1.74 (1.31), residues: 14 loop : -0.76 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.002 0.001 HIS A 360 PHE 0.007 0.001 PHE A 156 TYR 0.006 0.001 TYR A 137 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.398 Fit side-chains REVERT: B 30 ARG cc_start: 0.7450 (tpp80) cc_final: 0.6419 (mmm160) REVERT: B 55 LYS cc_start: 0.8272 (tttt) cc_final: 0.7891 (tttp) REVERT: A 77 MET cc_start: 0.8370 (mmt) cc_final: 0.7997 (mmt) REVERT: A 82 SER cc_start: 0.8866 (t) cc_final: 0.8576 (t) REVERT: A 264 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7862 (mm-30) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 0.2037 time to fit residues: 14.5417 Evaluate side-chains 59 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 264 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7558 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4276 Z= 0.263 Angle : 0.563 6.298 5790 Z= 0.276 Chirality : 0.039 0.130 677 Planarity : 0.004 0.039 709 Dihedral : 5.065 27.208 594 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.79 % Allowed : 10.49 % Favored : 87.72 % 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: 2.72 (0.37), residues: 522 helix: 2.61 (0.25), residues: 396 sheet: -1.72 (1.34), residues: 14 loop : -0.79 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.003 0.001 HIS A 360 PHE 0.009 0.001 PHE A 252 TYR 0.017 0.001 TYR A 336 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.515 Fit side-chains REVERT: B 30 ARG cc_start: 0.7499 (tpp80) cc_final: 0.6412 (mmm160) REVERT: B 55 LYS cc_start: 0.8359 (tttt) cc_final: 0.8005 (tttp) REVERT: A 24 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5174 (mmt180) REVERT: A 77 MET cc_start: 0.8428 (mmt) cc_final: 0.8045 (mmt) REVERT: A 82 SER cc_start: 0.8920 (t) cc_final: 0.8603 (t) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.2237 time to fit residues: 16.2973 Evaluate side-chains 60 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 463 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 51 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.7531 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4276 Z= 0.200 Angle : 0.540 7.231 5790 Z= 0.264 Chirality : 0.038 0.125 677 Planarity : 0.004 0.039 709 Dihedral : 5.084 26.794 594 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.79 % Allowed : 11.38 % Favored : 86.83 % 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: 2.80 (0.37), residues: 522 helix: 2.67 (0.26), residues: 395 sheet: -1.50 (1.36), residues: 14 loop : -0.76 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE A 252 TYR 0.006 0.001 TYR A 137 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.492 Fit side-chains REVERT: B 30 ARG cc_start: 0.7482 (tpp80) cc_final: 0.6394 (mmm160) REVERT: B 55 LYS cc_start: 0.8325 (tttt) cc_final: 0.7964 (tttp) REVERT: A 77 MET cc_start: 0.8380 (mmt) cc_final: 0.7997 (mmt) REVERT: A 82 SER cc_start: 0.8911 (t) cc_final: 0.8602 (t) REVERT: A 264 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7935 (mm-30) REVERT: A 368 MET cc_start: 0.7396 (tpt) cc_final: 0.7158 (tpt) outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.2067 time to fit residues: 15.0020 Evaluate side-chains 61 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 463 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 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: 0.7551 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4276 Z= 0.231 Angle : 0.554 8.059 5790 Z= 0.270 Chirality : 0.039 0.130 677 Planarity : 0.004 0.039 709 Dihedral : 5.157 26.879 594 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.01 % Allowed : 11.61 % Favored : 86.38 % 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: 2.79 (0.37), residues: 522 helix: 2.66 (0.26), residues: 395 sheet: -1.49 (1.41), residues: 14 loop : -0.77 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.003 0.001 HIS A 360 PHE 0.009 0.001 PHE A 252 TYR 0.006 0.001 TYR A 131 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.522 Fit side-chains REVERT: B 30 ARG cc_start: 0.7517 (tpp80) cc_final: 0.6403 (mmm160) REVERT: B 55 LYS cc_start: 0.8359 (tttt) cc_final: 0.8010 (tttp) REVERT: A 24 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.5102 (mmt180) REVERT: A 65 MET cc_start: 0.8479 (mmt) cc_final: 0.8271 (mmm) REVERT: A 77 MET cc_start: 0.8394 (mmt) cc_final: 0.7998 (mmt) REVERT: A 82 SER cc_start: 0.8923 (t) cc_final: 0.8607 (t) REVERT: A 264 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7949 (mm-30) outliers start: 9 outliers final: 6 residues processed: 63 average time/residue: 0.2140 time to fit residues: 16.5208 Evaluate side-chains 64 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 463 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.7547 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4276 Z= 0.235 Angle : 0.565 8.864 5790 Z= 0.275 Chirality : 0.039 0.156 677 Planarity : 0.004 0.039 709 Dihedral : 5.223 27.071 594 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.56 % Allowed : 13.17 % Favored : 85.27 % 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: 2.80 (0.37), residues: 522 helix: 2.66 (0.26), residues: 395 sheet: -1.43 (1.44), residues: 14 loop : -0.75 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.002 0.001 HIS A 360 PHE 0.009 0.001 PHE A 252 TYR 0.006 0.001 TYR A 137 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.494 Fit side-chains REVERT: B 30 ARG cc_start: 0.7525 (tpp80) cc_final: 0.6405 (mmm160) REVERT: B 55 LYS cc_start: 0.8357 (tttt) cc_final: 0.8023 (tttp) REVERT: A 65 MET cc_start: 0.8484 (mmt) cc_final: 0.8278 (mmm) REVERT: A 77 MET cc_start: 0.8391 (mmt) cc_final: 0.7989 (mmt) REVERT: A 82 SER cc_start: 0.8913 (t) cc_final: 0.8599 (t) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.2079 time to fit residues: 15.9843 Evaluate side-chains 62 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 463 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7542 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4276 Z= 0.222 Angle : 0.570 9.107 5790 Z= 0.277 Chirality : 0.039 0.154 677 Planarity : 0.004 0.039 709 Dihedral : 5.294 28.676 594 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.56 % Allowed : 13.84 % Favored : 84.60 % 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: 2.80 (0.37), residues: 522 helix: 2.67 (0.26), residues: 395 sheet: -1.47 (1.42), residues: 14 loop : -0.76 (0.55), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.002 0.001 HIS A 360 PHE 0.011 0.001 PHE A 119 TYR 0.006 0.001 TYR A 131 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.475 Fit side-chains REVERT: B 30 ARG cc_start: 0.7529 (tpp80) cc_final: 0.6398 (mmm160) REVERT: B 55 LYS cc_start: 0.8352 (tttt) cc_final: 0.8006 (tttp) REVERT: A 65 MET cc_start: 0.8513 (mmt) cc_final: 0.8302 (mmm) REVERT: A 77 MET cc_start: 0.8388 (mmt) cc_final: 0.7989 (mmt) REVERT: A 82 SER cc_start: 0.8894 (t) cc_final: 0.8581 (t) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.2056 time to fit residues: 15.9058 Evaluate side-chains 62 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 463 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.0570 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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: 0.7530 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4276 Z= 0.206 Angle : 0.564 9.567 5790 Z= 0.275 Chirality : 0.039 0.153 677 Planarity : 0.004 0.040 709 Dihedral : 5.356 30.924 594 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.34 % Allowed : 14.06 % Favored : 84.60 % 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: 522 helix: 2.70 (0.26), residues: 395 sheet: -1.36 (1.44), residues: 14 loop : -0.75 (0.55), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.002 0.001 HIS A 360 PHE 0.009 0.001 PHE A 119 TYR 0.006 0.001 TYR A 455 ARG 0.004 0.000 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.509 Fit side-chains REVERT: B 30 ARG cc_start: 0.7532 (tpp80) cc_final: 0.6391 (mmm160) REVERT: B 55 LYS cc_start: 0.8319 (tttt) cc_final: 0.7967 (tttp) REVERT: A 65 MET cc_start: 0.8509 (mmt) cc_final: 0.8300 (mmm) REVERT: A 77 MET cc_start: 0.8349 (mmt) cc_final: 0.7960 (mmt) REVERT: A 82 SER cc_start: 0.8881 (t) cc_final: 0.8572 (t) REVERT: A 311 ARG cc_start: 0.6112 (mtm180) cc_final: 0.5899 (mtp180) outliers start: 6 outliers final: 6 residues processed: 61 average time/residue: 0.2010 time to fit residues: 15.1929 Evaluate side-chains 62 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 463 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.149475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117597 restraints weight = 4756.997| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.18 r_work: 0.3205 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4276 Z= 0.260 Angle : 0.595 9.171 5790 Z= 0.289 Chirality : 0.040 0.150 677 Planarity : 0.004 0.039 709 Dihedral : 5.470 31.781 594 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.01 % Allowed : 14.29 % Favored : 83.71 % 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: 2.74 (0.37), residues: 522 helix: 2.62 (0.26), residues: 395 sheet: -1.51 (1.44), residues: 14 loop : -0.72 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.003 0.001 HIS A 360 PHE 0.011 0.001 PHE A 119 TYR 0.007 0.001 TYR A 137 ARG 0.004 0.000 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1311.15 seconds wall clock time: 24 minutes 58.58 seconds (1498.58 seconds total)