Starting phenix.real_space_refine on Tue Jan 14 22:43:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bi9_44577/01_2025/9bi9_44577.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bi9_44577/01_2025/9bi9_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_44577/01_2025/9bi9_44577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bi9_44577/01_2025/9bi9_44577.map" model { file = "/net/cci-nas-00/data/ceres_data/9bi9_44577/01_2025/9bi9_44577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bi9_44577/01_2025/9bi9_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-5571/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: 4.15, per 1000 atoms: 0.55 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: 1.96 Conformation dependent library (CDL) restraints added in 729.6 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: 0.70 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: 2.44 Time building geometry restraints manager: 2.31 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: 0.990 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.650 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: 0.000 Load rotamer database and sin/cos tables:10.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.600 ------------------------------------------------------------------------------- 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 : 0.571 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: 2.6630 time to fit residues: 260.5818 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 : 0.703 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.096918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.077272 restraints weight = 20872.884| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.81 r_work: 0.3009 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9349 (tp40) cc_final: 0.9116 (tm-30) REVERT: A 207 LYS cc_start: 0.7732 (tmmt) cc_final: 0.7432 (ttmm) REVERT: A 242 ASP cc_start: 0.8812 (t70) cc_final: 0.8569 (t0) REVERT: A 496 ASP cc_start: 0.8813 (t0) cc_final: 0.8478 (t0) outliers start: 3 outliers final: 0 residues processed: 60 average time/residue: 2.5834 time to fit residues: 160.2432 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 : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.0070 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.097027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.077201 restraints weight = 20691.437| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.80 r_work: 0.2999 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3968 Z= 0.154 Angle : 0.542 4.393 5393 Z= 0.266 Chirality : 0.038 0.127 586 Planarity : 0.006 0.083 700 Dihedral : 3.879 15.056 535 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.72 % Allowed : 13.16 % Favored : 86.12 % 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 (0.38), residues: 495 helix: 2.24 (0.36), residues: 214 sheet: -1.62 (0.66), residues: 53 loop : -0.54 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 29 HIS 0.003 0.001 HIS A 124 PHE 0.006 0.001 PHE A 482 TYR 0.008 0.001 TYR A 455 ARG 0.009 0.001 ARG A 397 *********************** 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 56 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9353 (tp40) cc_final: 0.9095 (tm-30) REVERT: A 207 LYS cc_start: 0.7639 (tmmt) cc_final: 0.7158 (mttm) REVERT: A 242 ASP cc_start: 0.8828 (t70) cc_final: 0.8476 (t0) REVERT: A 493 TRP cc_start: 0.7444 (t-100) cc_final: 0.7205 (t-100) REVERT: A 496 ASP cc_start: 0.8680 (t0) cc_final: 0.8300 (t0) outliers start: 3 outliers final: 1 residues processed: 54 average time/residue: 2.1237 time to fit residues: 119.6162 Evaluate side-chains 48 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.095842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.076350 restraints weight = 20529.775| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.77 r_work: 0.2993 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3035 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= 0.165 Angle : 0.526 4.630 5393 Z= 0.258 Chirality : 0.038 0.124 586 Planarity : 0.005 0.045 700 Dihedral : 3.745 14.891 535 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.20 % Allowed : 13.88 % 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: 0.96 (0.38), residues: 495 helix: 2.36 (0.36), residues: 213 sheet: -1.53 (0.67), residues: 53 loop : -0.46 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 29 HIS 0.002 0.001 HIS A 124 PHE 0.006 0.001 PHE A 265 TYR 0.010 0.001 TYR A 455 ARG 0.005 0.000 ARG A 397 *********************** 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 60 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9353 (tp40) cc_final: 0.9113 (tm-30) REVERT: A 207 LYS cc_start: 0.7653 (tmmt) cc_final: 0.7179 (mttp) REVERT: A 221 MET cc_start: 0.7130 (mmt) cc_final: 0.6894 (mtt) REVERT: A 242 ASP cc_start: 0.8882 (t70) cc_final: 0.8565 (t0) outliers start: 5 outliers final: 3 residues processed: 58 average time/residue: 2.3224 time to fit residues: 139.7515 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 : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 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 12 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.093020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.073461 restraints weight = 20805.554| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.77 r_work: 0.2942 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3968 Z= 0.262 Angle : 0.554 4.402 5393 Z= 0.277 Chirality : 0.039 0.125 586 Planarity : 0.005 0.047 700 Dihedral : 3.838 15.044 535 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: 0.79 (0.38), residues: 495 helix: 2.20 (0.36), residues: 213 sheet: -1.58 (0.69), residues: 53 loop : -0.54 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 29 HIS 0.003 0.001 HIS A 124 PHE 0.008 0.001 PHE A 265 TYR 0.013 0.001 TYR A 455 ARG 0.005 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 57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9364 (tp40) cc_final: 0.9119 (tm-30) REVERT: A 207 LYS cc_start: 0.7717 (tmmt) cc_final: 0.7232 (mttp) REVERT: A 221 MET cc_start: 0.7244 (mmt) cc_final: 0.7020 (mtt) REVERT: A 242 ASP cc_start: 0.8926 (t70) cc_final: 0.8594 (t0) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 2.1204 time to fit residues: 114.8733 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 : 0.645 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.093445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.073758 restraints weight = 20626.410| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.77 r_work: 0.2938 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3968 Z= 0.188 Angle : 0.532 4.686 5393 Z= 0.263 Chirality : 0.038 0.124 586 Planarity : 0.005 0.051 700 Dihedral : 3.782 14.923 535 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.20 % Allowed : 14.83 % 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: 0.85 (0.38), residues: 495 helix: 2.27 (0.36), residues: 212 sheet: -1.51 (0.70), residues: 53 loop : -0.53 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 29 HIS 0.003 0.001 HIS A 124 PHE 0.008 0.001 PHE A 487 TYR 0.015 0.001 TYR A 455 ARG 0.007 0.000 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 56 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9363 (tp40) cc_final: 0.9112 (tm-30) REVERT: A 207 LYS cc_start: 0.7688 (tmmt) cc_final: 0.7184 (mttp) REVERT: A 242 ASP cc_start: 0.8937 (t70) cc_final: 0.8582 (t0) REVERT: A 344 ASP cc_start: 0.8823 (m-30) cc_final: 0.8218 (m-30) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 2.0790 time to fit residues: 114.8742 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 : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.093844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.074198 restraints weight = 20298.355| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.75 r_work: 0.2961 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3532 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= 0.170 Angle : 0.527 4.687 5393 Z= 0.260 Chirality : 0.038 0.124 586 Planarity : 0.005 0.055 700 Dihedral : 3.731 14.978 535 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.72 % Allowed : 15.07 % Favored : 84.21 % 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: 0.92 (0.38), residues: 495 helix: 2.32 (0.37), residues: 212 sheet: -1.49 (0.71), residues: 53 loop : -0.48 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 493 HIS 0.002 0.001 HIS A 124 PHE 0.006 0.001 PHE A 265 TYR 0.011 0.001 TYR A 455 ARG 0.008 0.000 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 52 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9363 (tp40) cc_final: 0.9113 (tm-30) REVERT: A 207 LYS cc_start: 0.7706 (tmmt) cc_final: 0.7206 (mttp) REVERT: A 242 ASP cc_start: 0.8954 (t70) cc_final: 0.8626 (t0) REVERT: A 344 ASP cc_start: 0.8828 (m-30) cc_final: 0.8234 (m-30) outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 2.2208 time to fit residues: 117.9988 Evaluate side-chains 49 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.093655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074009 restraints weight = 20784.479| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.80 r_work: 0.2964 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3968 Z= 0.195 Angle : 0.539 5.135 5393 Z= 0.265 Chirality : 0.038 0.124 586 Planarity : 0.005 0.060 700 Dihedral : 3.752 14.956 535 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: 0.80 (0.38), residues: 495 helix: 2.08 (0.37), residues: 219 sheet: -1.52 (0.70), residues: 53 loop : -0.48 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 493 HIS 0.002 0.001 HIS A 124 PHE 0.009 0.001 PHE A 487 TYR 0.016 0.001 TYR A 455 ARG 0.008 0.001 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 52 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9362 (tp40) cc_final: 0.9109 (tm-30) REVERT: A 207 LYS cc_start: 0.7717 (tmmt) cc_final: 0.7210 (mttp) REVERT: A 242 ASP cc_start: 0.8978 (t70) cc_final: 0.8658 (t0) REVERT: A 344 ASP cc_start: 0.8847 (m-30) cc_final: 0.8248 (m-30) outliers start: 4 outliers final: 4 residues processed: 51 average time/residue: 2.0852 time to fit residues: 110.8604 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 : 0.582 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.093365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.073531 restraints weight = 20951.604| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.84 r_work: 0.2959 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3968 Z= 0.183 Angle : 0.548 6.385 5393 Z= 0.271 Chirality : 0.038 0.124 586 Planarity : 0.005 0.061 700 Dihedral : 3.735 15.081 535 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.96 % Allowed : 15.55 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.38), residues: 495 helix: 2.08 (0.37), residues: 219 sheet: -1.50 (0.71), residues: 53 loop : -0.47 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 493 HIS 0.002 0.001 HIS A 124 PHE 0.007 0.001 PHE A 265 TYR 0.014 0.001 TYR A 455 ARG 0.009 0.001 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 52 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9369 (tp40) cc_final: 0.9110 (tm-30) REVERT: A 207 LYS cc_start: 0.7695 (tmmt) cc_final: 0.7188 (mttp) REVERT: A 242 ASP cc_start: 0.8980 (t70) cc_final: 0.8654 (t0) REVERT: A 344 ASP cc_start: 0.8834 (m-30) cc_final: 0.8232 (m-30) outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 2.2451 time to fit residues: 116.6818 Evaluate side-chains 50 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.093673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.073916 restraints weight = 20735.900| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.81 r_work: 0.2959 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3851 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= 0.174 Angle : 0.552 6.181 5393 Z= 0.272 Chirality : 0.038 0.123 586 Planarity : 0.005 0.064 700 Dihedral : 3.725 15.104 535 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.72 % Allowed : 16.27 % 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: 0.70 (0.38), residues: 495 helix: 2.05 (0.37), residues: 219 sheet: -1.79 (0.77), residues: 44 loop : -0.62 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 493 HIS 0.002 0.001 HIS A 124 PHE 0.014 0.001 PHE A 487 TYR 0.013 0.001 TYR A 455 ARG 0.010 0.001 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 52 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9364 (tp40) cc_final: 0.9106 (tm-30) REVERT: A 207 LYS cc_start: 0.7704 (tmmt) cc_final: 0.7210 (mttp) REVERT: A 242 ASP cc_start: 0.8989 (t70) cc_final: 0.8672 (t0) REVERT: A 344 ASP cc_start: 0.8829 (m-30) cc_final: 0.8234 (m-30) outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 2.3138 time to fit residues: 122.5733 Evaluate side-chains 49 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3360 r_free = 0.3360 target = 0.091538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.071695 restraints weight = 20673.314| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.81 r_work: 0.2884 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3882 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= 0.253 Angle : 0.581 6.349 5393 Z= 0.290 Chirality : 0.039 0.128 586 Planarity : 0.005 0.064 700 Dihedral : 3.833 14.704 535 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.96 % Allowed : 16.51 % Favored : 82.54 % 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: 0.53 (0.38), residues: 495 helix: 1.92 (0.37), residues: 219 sheet: -1.80 (0.77), residues: 41 loop : -0.76 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 493 HIS 0.003 0.001 HIS A 124 PHE 0.008 0.001 PHE A 265 TYR 0.014 0.001 TYR A 455 ARG 0.008 0.001 ARG A 477 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6272.66 seconds wall clock time: 111 minutes 10.12 seconds (6670.12 seconds total)