Starting phenix.real_space_refine on Sat Dec 28 03:13:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bi9_44577/12_2024/9bi9_44577.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bi9_44577/12_2024/9bi9_44577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bi9_44577/12_2024/9bi9_44577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bi9_44577/12_2024/9bi9_44577.map" model { file = "/net/cci-nas-00/data/ceres_data/9bi9_44577/12_2024/9bi9_44577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bi9_44577/12_2024/9bi9_44577.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians Mg 1 5.21 5 S 21 5.16 5 C 2457 2.51 5 N 663 2.21 5 O 724 1.98 5 H 3712 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7578 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 7577 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 39, 'TRANS': 457} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.45, per 1000 atoms: 0.59 Number of scatterers: 7578 At special positions: 0 Unit cell: (67.32, 77.88, 77.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 Mg 1 11.99 O 724 8.00 N 663 7.00 C 2457 6.00 H 3712 1.00 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: 2.20 Conformation dependent library (CDL) restraints added in 750.1 milliseconds 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 922 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 6 sheets defined 48.3% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 69 through 72 Processing helix chain 'A' and resid 79 through 98 removed outlier: 3.810A pdb=" N ALA A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.723A pdb=" N LEU A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.518A pdb=" N TRP A 131 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 154 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 188 through 209 removed outlier: 5.878A pdb=" N GLY A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 233 Proline residue: A 226 - end of helix removed outlier: 3.870A pdb=" N GLU A 230 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 251 through 266 Processing helix chain 'A' and resid 268 through 281 removed outlier: 4.226A pdb=" N ILE A 274 " --> pdb=" O HIS A 270 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 325 Processing helix chain 'A' and resid 328 through 335 Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 407 through 414 removed outlier: 3.529A pdb=" N GLN A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 Processing helix chain 'A' and resid 451 through 469 removed outlier: 3.520A pdb=" N GLU A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 removed outlier: 6.542A pdb=" N GLN A 291 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 30 removed outlier: 5.327A pdb=" N LYS A 27 " --> pdb=" O GLY A 420 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA5, first strand: chain 'A' and resid 340 through 341 removed outlier: 4.270A pdb=" N ASP A 344 " --> pdb=" O TYR A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 390 190 hydrogen bonds defined for protein. 531 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: 2.87 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3705 1.03 - 1.23: 7 1.23 - 1.42: 1639 1.42 - 1.61: 2294 1.61 - 1.81: 35 Bond restraints: 7680 Sorted by residual: bond pdb=" CA VAL A 179 " pdb=" CB VAL A 179 " ideal model delta sigma weight residual 1.538 1.514 0.024 9.80e-03 1.04e+04 6.18e+00 bond pdb=" CA ILE A 431 " pdb=" CB ILE A 431 " ideal model delta sigma weight residual 1.546 1.536 0.010 8.80e-03 1.29e+04 1.36e+00 bond pdb=" CA THR A 117 " pdb=" CB THR A 117 " ideal model delta sigma weight residual 1.529 1.514 0.015 1.61e-02 3.86e+03 8.85e-01 bond pdb=" CA GLU A 152 " pdb=" CB GLU A 152 " ideal model delta sigma weight residual 1.528 1.517 0.012 1.56e-02 4.11e+03 5.50e-01 bond pdb=" CA ASN A 81 " pdb=" CB ASN A 81 " ideal model delta sigma weight residual 1.529 1.518 0.012 1.74e-02 3.30e+03 4.41e-01 ... (remaining 7675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 12800 0.99 - 1.97: 1005 1.97 - 2.96: 40 2.96 - 3.94: 30 3.94 - 4.93: 9 Bond angle restraints: 13884 Sorted by residual: angle pdb=" CA GLU A 152 " pdb=" CB GLU A 152 " pdb=" CG GLU A 152 " ideal model delta sigma weight residual 114.10 109.17 4.93 2.00e+00 2.50e-01 6.07e+00 angle pdb=" CB GLU A 152 " pdb=" CG GLU A 152 " pdb=" CD GLU A 152 " ideal model delta sigma weight residual 112.60 109.45 3.15 1.70e+00 3.46e-01 3.44e+00 angle pdb=" N ILE A 346 " pdb=" CA ILE A 346 " pdb=" C ILE A 346 " ideal model delta sigma weight residual 109.34 106.02 3.32 2.08e+00 2.31e-01 2.54e+00 angle pdb=" N SER A 339 " pdb=" CA SER A 339 " pdb=" C SER A 339 " ideal model delta sigma weight residual 110.80 107.42 3.38 2.13e+00 2.20e-01 2.52e+00 angle pdb=" CA ILE A 431 " pdb=" C ILE A 431 " pdb=" N PRO A 432 " ideal model delta sigma weight residual 117.57 119.07 -1.50 1.01e+00 9.80e-01 2.20e+00 ... (remaining 13879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 3298 16.43 - 32.86: 242 32.86 - 49.29: 87 49.29 - 65.72: 29 65.72 - 82.16: 6 Dihedral angle restraints: 3662 sinusoidal: 1992 harmonic: 1670 Sorted by residual: dihedral pdb=" CA HIS A 121 " pdb=" C HIS A 121 " pdb=" N PRO A 122 " pdb=" CA PRO A 122 " ideal model delta harmonic sigma weight residual -180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA GLU A 364 " pdb=" C GLU A 364 " pdb=" N TYR A 365 " pdb=" CA TYR A 365 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ALA A 198 " pdb=" C ALA A 198 " pdb=" N PHE A 199 " pdb=" CA PHE A 199 " ideal model delta harmonic sigma weight residual 180.00 -164.73 -15.27 0 5.00e+00 4.00e-02 9.32e+00 ... (remaining 3659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 364 0.026 - 0.053: 139 0.053 - 0.079: 41 0.079 - 0.105: 32 0.105 - 0.131: 10 Chirality restraints: 586 Sorted by residual: chirality pdb=" CA ILE A 346 " pdb=" N ILE A 346 " pdb=" C ILE A 346 " pdb=" CB ILE A 346 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE A 294 " pdb=" N ILE A 294 " pdb=" C ILE A 294 " pdb=" CB ILE A 294 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA PRO A 122 " pdb=" N PRO A 122 " pdb=" C PRO A 122 " pdb=" CB PRO A 122 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 583 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 371 " -0.046 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO A 372 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 372 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 372 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 225 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO A 226 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 226 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 226 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 137 " -0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C THR A 137 " 0.018 2.00e-02 2.50e+03 pdb=" O THR A 137 " -0.007 2.00e-02 2.50e+03 pdb=" N GLY A 138 " -0.006 2.00e-02 2.50e+03 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 428 2.21 - 2.80: 15241 2.80 - 3.40: 19973 3.40 - 4.00: 25580 4.00 - 4.60: 39737 Nonbonded interactions: 100959 Sorted by model distance: nonbonded pdb=" O TRP A 246 " pdb="HE21 GLN A 250 " model vdw 1.608 2.450 nonbonded pdb=" O PHE A 28 " pdb=" HE2 HIS A 423 " model vdw 1.615 2.450 nonbonded pdb=" O SER A 118 " pdb=" HZ1 LYS A 127 " model vdw 1.617 2.450 nonbonded pdb="HD21 ASN A 220 " pdb=" OE2 GLU A 223 " model vdw 1.624 2.450 nonbonded pdb="HH12 ARG A 74 " pdb=" O SER A 248 " model vdw 1.650 2.450 ... (remaining 100954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.130 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.060 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3968 Z= 0.172 Angle : 0.528 4.929 5393 Z= 0.264 Chirality : 0.038 0.131 586 Planarity : 0.004 0.070 700 Dihedral : 12.519 82.156 1477 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.82 (0.39), residues: 495 helix: 2.16 (0.37), residues: 212 sheet: -1.30 (0.68), residues: 53 loop : -0.52 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 29 HIS 0.004 0.001 HIS A 423 PHE 0.005 0.001 PHE A 265 TYR 0.007 0.001 TYR A 239 ARG 0.002 0.000 ARG A 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue MET 471 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9190 (tp40) cc_final: 0.8990 (tm-30) REVERT: A 149 LEU cc_start: 0.9270 (tt) cc_final: 0.9053 (tp) REVERT: A 157 MET cc_start: 0.7865 (mtp) cc_final: 0.7483 (mtp) REVERT: A 207 LYS cc_start: 0.7473 (tmmt) cc_final: 0.7209 (ttmm) REVERT: A 242 ASP cc_start: 0.8289 (t70) cc_final: 0.7943 (t0) REVERT: A 392 ARG cc_start: 0.8368 (mtm110) cc_final: 0.8053 (mtm-85) REVERT: A 396 THR cc_start: 0.8619 (m) cc_final: 0.8344 (p) REVERT: A 475 VAL cc_start: 0.9187 (m) cc_final: 0.8887 (m) outliers start: 0 outliers final: 1 residues processed: 95 average time/residue: 2.6482 time to fit residues: 259.4669 Evaluate side-chains 57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3968 Z= 0.266 Angle : 0.599 4.787 5393 Z= 0.300 Chirality : 0.039 0.128 586 Planarity : 0.005 0.051 700 Dihedral : 4.117 16.036 537 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.72 % Allowed : 11.24 % Favored : 88.04 % 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: 0.55 (0.38), residues: 495 helix: 1.94 (0.36), residues: 215 sheet: -1.49 (0.67), residues: 53 loop : -0.70 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 29 HIS 0.004 0.001 HIS A 124 PHE 0.009 0.001 PHE A 487 TYR 0.009 0.001 TYR A 239 ARG 0.013 0.001 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue MET 471 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9181 (tp40) cc_final: 0.8962 (tm-30) REVERT: A 157 MET cc_start: 0.7694 (mtp) cc_final: 0.7476 (mtp) REVERT: A 207 LYS cc_start: 0.7561 (tmmt) cc_final: 0.7276 (ttmm) REVERT: A 242 ASP cc_start: 0.8486 (t70) cc_final: 0.8225 (t0) REVERT: A 496 ASP cc_start: 0.8729 (t0) cc_final: 0.8402 (t0) outliers start: 3 outliers final: 0 residues processed: 60 average time/residue: 2.5074 time to fit residues: 155.9185 Evaluate side-chains 46 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.7631 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3968 Z= 0.312 Angle : 0.593 4.872 5393 Z= 0.299 Chirality : 0.040 0.125 586 Planarity : 0.007 0.086 700 Dihedral : 4.186 15.513 535 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.44 % Allowed : 12.92 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.37), residues: 495 helix: 1.79 (0.36), residues: 214 sheet: -1.80 (0.66), residues: 53 loop : -0.77 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 29 HIS 0.003 0.001 HIS A 124 PHE 0.008 0.001 PHE A 403 TYR 0.011 0.001 TYR A 455 ARG 0.009 0.001 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue MET 471 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9211 (tp40) cc_final: 0.8948 (tm-30) REVERT: A 157 MET cc_start: 0.7689 (mtp) cc_final: 0.7437 (mtp) REVERT: A 207 LYS cc_start: 0.7551 (tmmt) cc_final: 0.7263 (ttmm) REVERT: A 242 ASP cc_start: 0.8620 (t70) cc_final: 0.8257 (t0) outliers start: 6 outliers final: 4 residues processed: 56 average time/residue: 2.3981 time to fit residues: 139.9247 Evaluate side-chains 48 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 462 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.7631 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3968 Z= 0.274 Angle : 0.571 4.467 5393 Z= 0.287 Chirality : 0.039 0.125 586 Planarity : 0.005 0.043 700 Dihedral : 4.089 15.366 535 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.20 % Allowed : 13.40 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.37), residues: 495 helix: 1.84 (0.36), residues: 214 sheet: -1.76 (0.69), residues: 53 loop : -0.80 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 29 HIS 0.004 0.001 HIS A 124 PHE 0.008 0.001 PHE A 265 TYR 0.010 0.001 TYR A 455 ARG 0.007 0.001 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue MET 471 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9212 (tp40) cc_final: 0.8947 (tm-30) REVERT: A 157 MET cc_start: 0.7673 (mtp) cc_final: 0.7428 (mtp) REVERT: A 207 LYS cc_start: 0.7533 (tmmt) cc_final: 0.7228 (ttmm) REVERT: A 221 MET cc_start: 0.7270 (mmt) cc_final: 0.7055 (mtt) REVERT: A 242 ASP cc_start: 0.8658 (t70) cc_final: 0.8303 (t0) REVERT: A 493 TRP cc_start: 0.7430 (t-100) cc_final: 0.7111 (t-100) outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 2.2078 time to fit residues: 119.6898 Evaluate side-chains 50 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 462 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.7631 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3968 Z= 0.263 Angle : 0.565 4.649 5393 Z= 0.283 Chirality : 0.039 0.124 586 Planarity : 0.005 0.049 700 Dihedral : 4.047 15.512 535 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.20 % Allowed : 14.11 % Favored : 84.69 % 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: 0.40 (0.37), residues: 495 helix: 1.86 (0.36), residues: 214 sheet: -1.76 (0.68), residues: 53 loop : -0.76 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 29 HIS 0.004 0.001 HIS A 124 PHE 0.008 0.001 PHE A 265 TYR 0.013 0.001 TYR A 455 ARG 0.006 0.001 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue MET 471 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9214 (tp40) cc_final: 0.8944 (tm-30) REVERT: A 157 MET cc_start: 0.7578 (mtp) cc_final: 0.7363 (mtp) REVERT: A 207 LYS cc_start: 0.7524 (tmmt) cc_final: 0.7212 (ttmm) REVERT: A 242 ASP cc_start: 0.8687 (t70) cc_final: 0.8323 (t0) outliers start: 5 outliers final: 5 residues processed: 54 average time/residue: 2.2000 time to fit residues: 123.9534 Evaluate side-chains 49 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 462 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.0470 chunk 47 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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: 0.7602 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3968 Z= 0.158 Angle : 0.532 4.457 5393 Z= 0.263 Chirality : 0.038 0.124 586 Planarity : 0.005 0.052 700 Dihedral : 3.851 15.559 535 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.96 % Allowed : 15.31 % Favored : 83.73 % 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: 0.73 (0.38), residues: 495 helix: 2.20 (0.37), residues: 213 sheet: -1.72 (0.68), residues: 53 loop : -0.60 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 29 HIS 0.003 0.001 HIS A 124 PHE 0.007 0.001 PHE A 482 TYR 0.014 0.001 TYR A 455 ARG 0.007 0.001 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue MET 471 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9206 (tp40) cc_final: 0.8943 (tm-30) REVERT: A 157 MET cc_start: 0.7473 (mtp) cc_final: 0.7261 (mtp) REVERT: A 207 LYS cc_start: 0.7519 (tmmt) cc_final: 0.7060 (mttp) REVERT: A 242 ASP cc_start: 0.8683 (t70) cc_final: 0.8319 (t0) REVERT: A 344 ASP cc_start: 0.8535 (m-30) cc_final: 0.7859 (m-30) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 2.2394 time to fit residues: 121.4892 Evaluate side-chains 50 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 462 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3968 Z= 0.208 Angle : 0.553 7.189 5393 Z= 0.275 Chirality : 0.038 0.124 586 Planarity : 0.005 0.058 700 Dihedral : 3.847 15.282 535 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.96 % Allowed : 14.11 % Favored : 84.93 % 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: 0.75 (0.38), residues: 495 helix: 2.19 (0.37), residues: 213 sheet: -1.73 (0.68), residues: 53 loop : -0.56 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 493 HIS 0.003 0.001 HIS A 124 PHE 0.008 0.001 PHE A 265 TYR 0.016 0.001 TYR A 455 ARG 0.008 0.001 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue MET 471 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9208 (tp40) cc_final: 0.8933 (tm-30) REVERT: A 157 MET cc_start: 0.7481 (mtp) cc_final: 0.7260 (mtp) REVERT: A 207 LYS cc_start: 0.7532 (tmmt) cc_final: 0.7063 (mttp) REVERT: A 242 ASP cc_start: 0.8707 (t70) cc_final: 0.8349 (t0) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 2.1621 time to fit residues: 119.9092 Evaluate side-chains 51 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 462 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.7626 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3968 Z= 0.246 Angle : 0.560 5.624 5393 Z= 0.279 Chirality : 0.039 0.125 586 Planarity : 0.005 0.063 700 Dihedral : 3.914 15.410 535 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.67 % Allowed : 14.35 % Favored : 83.97 % 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: 0.57 (0.38), residues: 495 helix: 1.92 (0.37), residues: 219 sheet: -1.64 (0.69), residues: 53 loop : -0.64 (0.38), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 493 HIS 0.003 0.001 HIS A 124 PHE 0.009 0.001 PHE A 487 TYR 0.012 0.001 TYR A 455 ARG 0.008 0.000 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue MET 471 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9211 (tp40) cc_final: 0.8931 (tm-30) REVERT: A 207 LYS cc_start: 0.7515 (tmmt) cc_final: 0.7172 (ttmm) REVERT: A 242 ASP cc_start: 0.8722 (t70) cc_final: 0.8364 (t0) outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 2.1547 time to fit residues: 123.4256 Evaluate side-chains 51 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 462 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 22 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.7615 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3968 Z= 0.194 Angle : 0.546 5.060 5393 Z= 0.271 Chirality : 0.039 0.123 586 Planarity : 0.005 0.063 700 Dihedral : 3.875 15.492 535 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.20 % Allowed : 15.79 % Favored : 83.01 % 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: 0.61 (0.38), residues: 495 helix: 2.02 (0.37), residues: 218 sheet: -1.65 (0.69), residues: 53 loop : -0.68 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 493 HIS 0.003 0.001 HIS A 124 PHE 0.007 0.001 PHE A 265 TYR 0.012 0.001 TYR A 455 ARG 0.008 0.000 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue MET 471 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9209 (tp40) cc_final: 0.8931 (tm-30) REVERT: A 207 LYS cc_start: 0.7528 (tmmt) cc_final: 0.7047 (mttp) REVERT: A 242 ASP cc_start: 0.8732 (t70) cc_final: 0.8363 (t0) outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 2.1645 time to fit residues: 117.4059 Evaluate side-chains 50 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 462 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7607 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3968 Z= 0.181 Angle : 0.542 4.934 5393 Z= 0.268 Chirality : 0.039 0.123 586 Planarity : 0.005 0.064 700 Dihedral : 3.813 15.567 535 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.67 % Allowed : 15.31 % Favored : 83.01 % 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: 0.56 (0.38), residues: 495 helix: 2.00 (0.37), residues: 219 sheet: -1.65 (0.70), residues: 55 loop : -0.73 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 493 HIS 0.003 0.001 HIS A 124 PHE 0.013 0.001 PHE A 487 TYR 0.018 0.001 TYR A 455 ARG 0.009 0.000 ARG A 477 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 21 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue MET 430 is missing expected H atoms. Skipping. Residue LYS 467 is missing expected H atoms. Skipping. Residue MET 471 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9204 (tp40) cc_final: 0.8929 (tm-30) REVERT: A 207 LYS cc_start: 0.7547 (tmmt) cc_final: 0.7221 (ttmm) REVERT: A 242 ASP cc_start: 0.8742 (t70) cc_final: 0.8378 (t0) REVERT: A 344 ASP cc_start: 0.8554 (m-30) cc_final: 0.7882 (m-30) outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 2.0848 time to fit residues: 117.5194 Evaluate side-chains 52 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 462 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 0.0060 chunk 19 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.094551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.074791 restraints weight = 20360.746| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.85 r_work: 0.2931 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3968 Z= 0.160 Angle : 0.537 4.994 5393 Z= 0.264 Chirality : 0.038 0.122 586 Planarity : 0.005 0.062 700 Dihedral : 3.731 15.438 535 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.72 % Allowed : 16.51 % Favored : 82.78 % 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: 0.63 (0.38), residues: 495 helix: 2.05 (0.37), residues: 219 sheet: -1.61 (0.70), residues: 55 loop : -0.68 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 493 HIS 0.002 0.001 HIS A 124 PHE 0.006 0.001 PHE A 265 TYR 0.016 0.001 TYR A 455 ARG 0.010 0.001 ARG A 477 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3840.85 seconds wall clock time: 68 minutes 49.76 seconds (4129.76 seconds total)