Starting phenix.real_space_refine on Tue Feb 13 08:27:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do1_27587/02_2024/8do1_27587_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do1_27587/02_2024/8do1_27587.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do1_27587/02_2024/8do1_27587_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do1_27587/02_2024/8do1_27587_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do1_27587/02_2024/8do1_27587_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do1_27587/02_2024/8do1_27587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do1_27587/02_2024/8do1_27587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do1_27587/02_2024/8do1_27587_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do1_27587/02_2024/8do1_27587_trim_updated.pdb" } resolution = 3.01 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= 0.044 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 2872 2.51 5 N 689 2.21 5 O 752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4339 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3548 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'SXF': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.94, per 1000 atoms: 0.68 Number of scatterers: 4339 At special positions: 0 Unit cell: (90.3, 76.65, 82.95, 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 752 8.00 N 689 7.00 C 2872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 816.2 milliseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1010 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 2 sheets defined 66.4% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.559A pdb=" N ILE A 9 " --> pdb=" O PHE A 5 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 28 through 45 Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 106 through 133 removed outlier: 3.517A pdb=" N LYS A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 143 No H-bonds generated for 'chain 'A' and resid 140 through 143' Processing helix chain 'A' and resid 145 through 171 Processing helix chain 'A' and resid 178 through 196 removed outlier: 3.504A pdb=" N ALA A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 242 through 259 Processing helix chain 'A' and resid 289 through 311 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 341 through 344 No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 358 through 382 removed outlier: 4.108A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 407 through 414 removed outlier: 4.361A pdb=" N TYR A 410 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 412 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 438 removed outlier: 3.510A pdb=" N SER A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 467 removed outlier: 3.564A pdb=" N SER A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 24 Processing helix chain 'B' and resid 30 through 65 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 71 through 95 removed outlier: 4.029A pdb=" N MET C 76 " --> pdb=" O PRO C 72 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 276 through 282 Processing sheet with id= B, first strand: chain 'A' and resid 323 through 325 removed outlier: 3.535A pdb=" N GLY A 339 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N SER A 325 " --> pdb=" O PRO A 337 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 807 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: 1.27 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 659 1.29 - 1.42: 1121 1.42 - 1.55: 2598 1.55 - 1.68: 12 1.68 - 1.81: 43 Bond restraints: 4433 Sorted by residual: bond pdb=" C54 SXF A 501 " pdb=" C55 SXF A 501 " ideal model delta sigma weight residual 0.000 1.532 -1.532 2.00e-02 2.50e+03 5.87e+03 bond pdb=" C34 SXF A 501 " pdb=" C36 SXF A 501 " ideal model delta sigma weight residual 0.454 1.503 -1.049 2.00e-02 2.50e+03 2.75e+03 bond pdb=" C44 SXF A 501 " pdb=" O43 SXF A 501 " ideal model delta sigma weight residual 0.475 1.464 -0.989 2.00e-02 2.50e+03 2.44e+03 bond pdb=" C44 SXF A 501 " pdb=" O45 SXF A 501 " ideal model delta sigma weight residual 1.954 1.401 0.553 2.00e-02 2.50e+03 7.65e+02 bond pdb=" C36 SXF A 501 " pdb=" C41 SXF A 501 " ideal model delta sigma weight residual 1.974 1.502 0.472 2.00e-02 2.50e+03 5.57e+02 ... (remaining 4428 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.86: 123 106.86 - 113.64: 2492 113.64 - 120.41: 1690 120.41 - 127.19: 1658 127.19 - 133.96: 38 Bond angle restraints: 6001 Sorted by residual: angle pdb=" C23 SXF A 501 " pdb=" C24 SXF A 501 " pdb=" C25 SXF A 501 " ideal model delta sigma weight residual 73.99 122.21 -48.22 3.00e+00 1.11e-01 2.58e+02 angle pdb=" C12 SXF A 501 " pdb=" C13 SXF A 501 " pdb=" C14 SXF A 501 " ideal model delta sigma weight residual 154.69 120.12 34.57 3.00e+00 1.11e-01 1.33e+02 angle pdb=" C24 SXF A 501 " pdb=" C26 SXF A 501 " pdb=" C27 SXF A 501 " ideal model delta sigma weight residual 109.06 120.54 -11.48 3.00e+00 1.11e-01 1.46e+01 angle pdb=" C04 SXF A 501 " pdb=" C05 SXF A 501 " pdb=" O06 SXF A 501 " ideal model delta sigma weight residual 110.24 120.16 -9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C11 SXF A 501 " pdb=" C12 SXF A 501 " pdb=" C13 SXF A 501 " ideal model delta sigma weight residual 111.76 121.67 -9.91 3.00e+00 1.11e-01 1.09e+01 ... (remaining 5996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 2565 34.45 - 68.89: 44 68.89 - 103.34: 8 103.34 - 137.78: 2 137.78 - 172.23: 3 Dihedral angle restraints: 2622 sinusoidal: 1047 harmonic: 1575 Sorted by residual: dihedral pdb=" C50 SXF A 501 " pdb=" C51 SXF A 501 " pdb=" C52 SXF A 501 " pdb=" C53 SXF A 501 " ideal model delta sinusoidal sigma weight residual 238.11 65.88 172.23 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C44 SXF A 501 " pdb=" C54 SXF A 501 " pdb=" O45 SXF A 501 " pdb=" C53 SXF A 501 " ideal model delta sinusoidal sigma weight residual -68.55 84.22 -152.77 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C04 SXF A 501 " pdb=" C02 SXF A 501 " pdb=" C03 SXF A 501 " pdb=" C48 SXF A 501 " ideal model delta sinusoidal sigma weight residual 120.85 -98.40 -140.75 1 3.00e+01 1.11e-03 1.89e+01 ... (remaining 2619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.282: 701 0.282 - 0.563: 4 0.563 - 0.845: 0 0.845 - 1.127: 2 1.127 - 1.408: 2 Chirality restraints: 709 Sorted by residual: chirality pdb=" C36 SXF A 501 " pdb=" C34 SXF A 501 " pdb=" C41 SXF A 501 " pdb=" O37 SXF A 501 " both_signs ideal model delta sigma weight residual False 1.13 2.54 -1.41 2.00e-01 2.50e+01 4.96e+01 chirality pdb=" C34 SXF A 501 " pdb=" C33 SXF A 501 " pdb=" C36 SXF A 501 " pdb=" O35 SXF A 501 " both_signs ideal model delta sigma weight residual False 1.20 2.49 -1.28 2.00e-01 2.50e+01 4.11e+01 chirality pdb=" C44 SXF A 501 " pdb=" C33 SXF A 501 " pdb=" O43 SXF A 501 " pdb=" O45 SXF A 501 " both_signs ideal model delta sigma weight residual False -1.41 -2.40 0.99 2.00e-01 2.50e+01 2.45e+01 ... (remaining 706 not shown) Planarity restraints: 734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 436 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" CG ASP A 436 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP A 436 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 436 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 71 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO C 72 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 72 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 72 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 16 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 17 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 17 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 17 " 0.018 5.00e-02 4.00e+02 ... (remaining 731 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 38 2.64 - 3.21: 4176 3.21 - 3.77: 7000 3.77 - 4.34: 9273 4.34 - 4.90: 15613 Nonbonded interactions: 36100 Sorted by model distance: nonbonded pdb=" OE1 GLU A 78 " pdb=" OH TYR A 137 " model vdw 2.081 2.440 nonbonded pdb=" O SER A 309 " pdb=" OG SER A 313 " model vdw 2.198 2.440 nonbonded pdb=" O GLY A 260 " pdb=" NH1 ARG A 262 " model vdw 2.275 2.520 nonbonded pdb=" OH TYR A 302 " pdb=" OG SER A 346 " model vdw 2.308 2.440 nonbonded pdb=" OD1 ASP B 17 " pdb=" NH2 ARG B 20 " model vdw 2.309 2.520 ... (remaining 36095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.650 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.300 Find NCS groups from input model: 0.120 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 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 : 0.039 1.532 4433 Z= 1.914 Angle : 1.033 48.223 6001 Z= 0.410 Chirality : 0.099 1.408 709 Planarity : 0.004 0.032 734 Dihedral : 15.708 172.228 1612 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.57 % 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: 2.03 (0.37), residues: 543 helix: 2.26 (0.26), residues: 391 sheet: -1.73 (1.15), residues: 14 loop : -1.07 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.001 0.001 HIS A 360 PHE 0.020 0.001 PHE A 209 TYR 0.005 0.001 TYR A 457 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.493 Fit side-chains REVERT: A 133 MET cc_start: 0.8347 (mmm) cc_final: 0.7938 (mmt) REVERT: A 235 TYR cc_start: 0.7127 (m-10) cc_final: 0.6886 (m-80) REVERT: B 16 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7798 (tttp) REVERT: B 38 MET cc_start: 0.6826 (mmt) cc_final: 0.6520 (mmp) outliers start: 1 outliers final: 1 residues processed: 78 average time/residue: 0.2145 time to fit residues: 20.3254 Evaluate side-chains 60 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.0508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 4433 Z= 0.344 Angle : 1.142 33.530 6001 Z= 0.427 Chirality : 0.045 0.406 709 Planarity : 0.004 0.038 734 Dihedral : 15.873 156.247 620 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.94 % Allowed : 3.88 % Favored : 94.18 % 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: 1.97 (0.36), residues: 543 helix: 2.22 (0.26), residues: 391 sheet: -1.76 (1.17), residues: 14 loop : -1.09 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 64 HIS 0.001 0.000 HIS A 218 PHE 0.016 0.001 PHE A 156 TYR 0.021 0.001 TYR A 336 ARG 0.003 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.510 Fit side-chains REVERT: A 133 MET cc_start: 0.8348 (mmm) cc_final: 0.7914 (mmt) REVERT: A 235 TYR cc_start: 0.7132 (m-10) cc_final: 0.6849 (m-80) REVERT: B 16 LYS cc_start: 0.8147 (ttpp) cc_final: 0.7714 (tttp) REVERT: B 38 MET cc_start: 0.6829 (mmt) cc_final: 0.6542 (mmp) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.2096 time to fit residues: 16.1726 Evaluate side-chains 67 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain B residue 57 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 33 optimal weight: 0.0670 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 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 402 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.0642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4433 Z= 0.235 Angle : 0.860 23.413 6001 Z= 0.343 Chirality : 0.039 0.184 709 Planarity : 0.004 0.040 734 Dihedral : 15.708 150.377 620 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.51 % Allowed : 4.53 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.37), residues: 543 helix: 2.24 (0.26), residues: 391 sheet: -1.15 (1.48), residues: 12 loop : -1.07 (0.51), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 PHE 0.015 0.001 PHE A 156 TYR 0.018 0.001 TYR A 336 ARG 0.003 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.459 Fit side-chains REVERT: A 65 MET cc_start: 0.7485 (ptm) cc_final: 0.7160 (ptm) REVERT: A 133 MET cc_start: 0.8368 (mmm) cc_final: 0.7944 (mmt) REVERT: A 235 TYR cc_start: 0.7073 (m-10) cc_final: 0.6821 (m-80) REVERT: B 16 LYS cc_start: 0.8151 (ttpp) cc_final: 0.7696 (tttp) REVERT: B 38 MET cc_start: 0.6827 (mmt) cc_final: 0.6557 (mmp) outliers start: 7 outliers final: 7 residues processed: 64 average time/residue: 0.2099 time to fit residues: 16.6133 Evaluate side-chains 63 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain B residue 57 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 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: 0.7238 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4433 Z= 0.262 Angle : 0.839 24.393 6001 Z= 0.333 Chirality : 0.039 0.169 709 Planarity : 0.004 0.037 734 Dihedral : 15.855 150.879 620 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.51 % Allowed : 5.39 % Favored : 93.10 % 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: 2.03 (0.37), residues: 543 helix: 2.21 (0.26), residues: 392 sheet: -1.17 (1.51), residues: 12 loop : -1.01 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.016 0.001 PHE A 156 TYR 0.020 0.001 TYR A 336 ARG 0.008 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.525 Fit side-chains REVERT: A 65 MET cc_start: 0.7453 (ptm) cc_final: 0.7229 (ptm) REVERT: A 133 MET cc_start: 0.8335 (mmm) cc_final: 0.7922 (mmt) REVERT: A 235 TYR cc_start: 0.6973 (m-10) cc_final: 0.6706 (m-80) REVERT: B 16 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7666 (tttp) REVERT: B 38 MET cc_start: 0.6777 (mmt) cc_final: 0.6524 (mmp) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.2083 time to fit residues: 16.0467 Evaluate side-chains 63 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 393 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 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: 0.7240 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4433 Z= 0.255 Angle : 0.807 23.404 6001 Z= 0.323 Chirality : 0.039 0.187 709 Planarity : 0.004 0.044 734 Dihedral : 15.831 150.250 620 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.51 % Allowed : 6.25 % Favored : 92.24 % 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: 2.02 (0.37), residues: 543 helix: 2.21 (0.26), residues: 392 sheet: -1.19 (1.55), residues: 12 loop : -1.01 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 PHE 0.017 0.001 PHE A 156 TYR 0.016 0.001 TYR A 336 ARG 0.007 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.436 Fit side-chains REVERT: A 65 MET cc_start: 0.7431 (ptm) cc_final: 0.7185 (ptm) REVERT: A 133 MET cc_start: 0.8335 (mmm) cc_final: 0.7925 (mmt) REVERT: A 235 TYR cc_start: 0.6881 (m-10) cc_final: 0.6573 (m-80) REVERT: B 16 LYS cc_start: 0.8144 (ttpp) cc_final: 0.7673 (tttp) REVERT: B 38 MET cc_start: 0.6828 (mmt) cc_final: 0.6572 (mmp) outliers start: 7 outliers final: 7 residues processed: 61 average time/residue: 0.2040 time to fit residues: 15.4886 Evaluate side-chains 63 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 393 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.0970 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.7240 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4433 Z= 0.255 Angle : 0.807 23.404 6001 Z= 0.323 Chirality : 0.039 0.187 709 Planarity : 0.004 0.044 734 Dihedral : 15.831 150.250 620 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.51 % Allowed : 6.25 % Favored : 92.24 % 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: 2.02 (0.37), residues: 543 helix: 2.21 (0.26), residues: 392 sheet: -1.19 (1.55), residues: 12 loop : -1.01 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 PHE 0.017 0.001 PHE A 156 TYR 0.016 0.001 TYR A 336 ARG 0.007 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.532 Fit side-chains REVERT: A 65 MET cc_start: 0.7431 (ptm) cc_final: 0.7185 (ptm) REVERT: A 133 MET cc_start: 0.8335 (mmm) cc_final: 0.7925 (mmt) REVERT: A 235 TYR cc_start: 0.6880 (m-10) cc_final: 0.6573 (m-80) REVERT: B 16 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7673 (tttp) REVERT: B 38 MET cc_start: 0.6829 (mmt) cc_final: 0.6572 (mmp) outliers start: 7 outliers final: 7 residues processed: 60 average time/residue: 0.1914 time to fit residues: 14.2928 Evaluate side-chains 63 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 393 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7240 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4433 Z= 0.255 Angle : 0.807 23.404 6001 Z= 0.323 Chirality : 0.039 0.187 709 Planarity : 0.004 0.044 734 Dihedral : 15.832 150.250 620 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.51 % Allowed : 6.25 % Favored : 92.24 % 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: 2.02 (0.37), residues: 543 helix: 2.21 (0.26), residues: 392 sheet: -1.19 (1.55), residues: 12 loop : -1.01 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 PHE 0.017 0.001 PHE A 156 TYR 0.016 0.001 TYR A 336 ARG 0.007 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.504 Fit side-chains REVERT: A 65 MET cc_start: 0.7431 (ptm) cc_final: 0.7186 (ptm) REVERT: A 133 MET cc_start: 0.8335 (mmm) cc_final: 0.7925 (mmt) REVERT: A 235 TYR cc_start: 0.6880 (m-10) cc_final: 0.6573 (m-80) REVERT: B 16 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7673 (tttp) REVERT: B 38 MET cc_start: 0.6829 (mmt) cc_final: 0.6572 (mmp) outliers start: 7 outliers final: 7 residues processed: 60 average time/residue: 0.2011 time to fit residues: 14.9624 Evaluate side-chains 63 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 393 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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: 0.7240 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4433 Z= 0.254 Angle : 0.807 23.403 6001 Z= 0.323 Chirality : 0.039 0.187 709 Planarity : 0.004 0.044 734 Dihedral : 15.828 150.249 620 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.51 % Allowed : 6.25 % Favored : 92.24 % 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: 2.02 (0.37), residues: 543 helix: 2.21 (0.26), residues: 392 sheet: -1.19 (1.55), residues: 12 loop : -1.01 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 PHE 0.017 0.001 PHE A 156 TYR 0.016 0.001 TYR A 336 ARG 0.007 0.000 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.483 Fit side-chains REVERT: A 65 MET cc_start: 0.7431 (ptm) cc_final: 0.7186 (ptm) REVERT: A 133 MET cc_start: 0.8335 (mmm) cc_final: 0.7925 (mmt) REVERT: A 235 TYR cc_start: 0.6880 (m-10) cc_final: 0.6573 (m-80) REVERT: B 16 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7673 (tttp) REVERT: B 38 MET cc_start: 0.6829 (mmt) cc_final: 0.6572 (mmp) outliers start: 7 outliers final: 7 residues processed: 60 average time/residue: 0.2129 time to fit residues: 15.8457 Evaluate side-chains 63 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 393 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7240 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4433 Z= 0.202 Angle : 0.776 21.907 6001 Z= 0.315 Chirality : 0.039 0.214 709 Planarity : 0.005 0.096 734 Dihedral : 15.917 150.107 620 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.51 % Allowed : 6.03 % Favored : 92.46 % 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: 2.08 (0.37), residues: 543 helix: 2.32 (0.26), residues: 388 sheet: -1.37 (1.55), residues: 12 loop : -1.08 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 379 HIS 0.002 0.001 HIS A 218 PHE 0.015 0.001 PHE A 234 TYR 0.020 0.001 TYR A 336 ARG 0.006 0.001 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.457 Fit side-chains REVERT: A 133 MET cc_start: 0.8328 (mmm) cc_final: 0.7925 (mmt) REVERT: A 235 TYR cc_start: 0.6772 (m-10) cc_final: 0.6531 (m-80) REVERT: B 16 LYS cc_start: 0.8126 (ttpp) cc_final: 0.7655 (tttp) REVERT: B 38 MET cc_start: 0.6724 (mmt) cc_final: 0.6483 (mmp) outliers start: 7 outliers final: 7 residues processed: 62 average time/residue: 0.2064 time to fit residues: 15.8282 Evaluate side-chains 63 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain B residue 57 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 0.0470 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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: 0.7244 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4433 Z= 0.217 Angle : 0.775 22.272 6001 Z= 0.315 Chirality : 0.039 0.182 709 Planarity : 0.005 0.087 734 Dihedral : 15.953 149.888 620 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.51 % Allowed : 6.68 % Favored : 91.81 % 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: 2.07 (0.37), residues: 543 helix: 2.30 (0.26), residues: 388 sheet: -1.58 (1.51), residues: 12 loop : -1.06 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.021 0.001 PHE A 234 TYR 0.018 0.001 TYR A 336 ARG 0.007 0.001 ARG B 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.533 Fit side-chains REVERT: A 133 MET cc_start: 0.8333 (mmm) cc_final: 0.7932 (mmt) REVERT: B 16 LYS cc_start: 0.8134 (ttpp) cc_final: 0.7655 (tttp) REVERT: B 38 MET cc_start: 0.6723 (mmt) cc_final: 0.6482 (mmp) outliers start: 7 outliers final: 7 residues processed: 61 average time/residue: 0.1985 time to fit residues: 15.0689 Evaluate side-chains 65 residues out of total 469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain B residue 57 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.166776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.127344 restraints weight = 6515.634| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.52 r_work: 0.3377 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4433 Z= 0.204 Angle : 0.759 21.755 6001 Z= 0.312 Chirality : 0.039 0.165 709 Planarity : 0.005 0.082 734 Dihedral : 15.964 149.696 620 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.51 % Allowed : 6.68 % Favored : 91.81 % 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: 2.08 (0.37), residues: 543 helix: 2.31 (0.26), residues: 388 sheet: -1.81 (1.47), residues: 12 loop : -1.01 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 379 HIS 0.002 0.001 HIS B 58 PHE 0.016 0.001 PHE A 234 TYR 0.019 0.001 TYR A 336 ARG 0.008 0.001 ARG B 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1277.45 seconds wall clock time: 23 minutes 46.29 seconds (1426.29 seconds total)