Starting phenix.real_space_refine on Wed Mar 12 07:50:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bi9_44577/03_2025/9bi9_44577.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bi9_44577/03_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_44577/03_2025/9bi9_44577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bi9_44577/03_2025/9bi9_44577.map" model { file = "/net/cci-nas-00/data/ceres_data/9bi9_44577/03_2025/9bi9_44577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bi9_44577/03_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-5624/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: 4.42, per 1000 atoms: 0.58 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 676.9 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: 0.66 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: 2.64 Time building geometry restraints manager: 2.40 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: 0.010 Normalize map: mean=0, sd=1: 1.590 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.970 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:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- 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 : 0.555 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: 2.5696 time to fit residues: 251.5192 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 : 0.602 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.096647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.076820 restraints weight = 20861.183| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.80 r_work: 0.3008 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 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 = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9348 (tp40) cc_final: 0.9115 (tm-30) REVERT: A 207 LYS cc_start: 0.7733 (tmmt) cc_final: 0.7433 (ttmm) REVERT: A 242 ASP cc_start: 0.8813 (t70) cc_final: 0.8569 (t0) REVERT: A 496 ASP cc_start: 0.8821 (t0) cc_final: 0.8483 (t0) outliers start: 3 outliers final: 0 residues processed: 60 average time/residue: 2.4318 time to fit residues: 150.8338 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 : 0.593 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.095544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.075639 restraints weight = 20775.507| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.79 r_work: 0.2989 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3968 Z= 0.183 Angle : 0.548 4.400 5393 Z= 0.270 Chirality : 0.038 0.126 586 Planarity : 0.006 0.084 700 Dihedral : 3.940 15.246 535 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.20 % Allowed : 12.68 % 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: 0.71 (0.38), residues: 495 helix: 2.14 (0.36), residues: 214 sheet: -1.68 (0.66), residues: 53 loop : -0.59 (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 0.009 0.001 TYR A 455 ARG 0.008 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 55 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9354 (tp40) cc_final: 0.9117 (tm-30) REVERT: A 207 LYS cc_start: 0.7681 (tmmt) cc_final: 0.7200 (mttm) REVERT: A 242 ASP cc_start: 0.8871 (t70) cc_final: 0.8530 (t0) REVERT: A 496 ASP cc_start: 0.8717 (t0) cc_final: 0.8418 (t0) outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 2.0603 time to fit residues: 111.9052 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 : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 0.0770 chunk 46 optimal weight: 3.9990 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: 0.4980 chunk 42 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.0742 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.094289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.074703 restraints weight = 20594.503| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.75 r_work: 0.2961 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3086 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= 0.197 Angle : 0.536 4.617 5393 Z= 0.266 Chirality : 0.038 0.125 586 Planarity : 0.005 0.046 700 Dihedral : 3.807 15.102 535 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: 0.78 (0.38), residues: 495 helix: 2.19 (0.36), residues: 213 sheet: -1.63 (0.68), residues: 53 loop : -0.52 (0.39), 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 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 57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9355 (tp40) cc_final: 0.9114 (tm-30) REVERT: A 207 LYS cc_start: 0.7700 (tmmt) cc_final: 0.7224 (mttp) REVERT: A 242 ASP cc_start: 0.8900 (t70) cc_final: 0.8589 (t0) REVERT: A 493 TRP cc_start: 0.7438 (t-100) cc_final: 0.7194 (t-100) REVERT: A 496 ASP cc_start: 0.8687 (t0) cc_final: 0.8380 (t0) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 2.2370 time to fit residues: 125.5538 Evaluate side-chains 48 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR 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: 4.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.091136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.071421 restraints weight = 20925.405| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.79 r_work: 0.2901 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3968 Z= 0.307 Angle : 0.584 5.240 5393 Z= 0.295 Chirality : 0.040 0.126 586 Planarity : 0.006 0.052 700 Dihedral : 4.021 15.586 535 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.96 % Allowed : 13.88 % Favored : 85.17 % 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: 0.47 (0.38), residues: 495 helix: 1.88 (0.36), residues: 214 sheet: -1.66 (0.70), residues: 53 loop : -0.70 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 493 HIS 0.003 0.001 HIS A 124 PHE 0.009 0.001 PHE A 265 TYR 0.014 0.002 TYR A 455 ARG 0.007 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 52 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9370 (tp40) cc_final: 0.9107 (tm-30) REVERT: A 207 LYS cc_start: 0.7729 (tmmt) cc_final: 0.7381 (ttmm) REVERT: A 242 ASP cc_start: 0.8947 (t70) cc_final: 0.8630 (t0) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 2.2893 time to fit residues: 119.0688 Evaluate side-chains 49 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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: 0.7980 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.091975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.072067 restraints weight = 20587.953| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.77 r_work: 0.2924 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3968 Z= 0.218 Angle : 0.549 4.494 5393 Z= 0.274 Chirality : 0.039 0.124 586 Planarity : 0.005 0.051 700 Dihedral : 3.873 15.295 535 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.67 % Allowed : 13.64 % 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: 0.56 (0.38), residues: 495 helix: 2.07 (0.37), residues: 213 sheet: -1.92 (0.75), residues: 41 loop : -0.77 (0.37), residues: 241 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 0.007 0.001 PHE A 482 TYR 0.009 0.001 TYR A 455 ARG 0.008 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 57 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9367 (tp40) cc_final: 0.9105 (tm-30) REVERT: A 207 LYS cc_start: 0.7699 (tmmt) cc_final: 0.7199 (mttp) REVERT: A 242 ASP cc_start: 0.8952 (t70) cc_final: 0.8593 (t0) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 2.1084 time to fit residues: 114.1755 Evaluate side-chains 52 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 157 MET 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: 1.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.091907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.072285 restraints weight = 20444.844| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.73 r_work: 0.2926 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3665 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= 0.232 Angle : 0.559 7.059 5393 Z= 0.280 Chirality : 0.039 0.125 586 Planarity : 0.005 0.058 700 Dihedral : 3.862 15.298 535 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.44 % Allowed : 13.40 % Favored : 85.17 % 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 (0.37), residues: 495 helix: 2.03 (0.37), residues: 213 sheet: -1.92 (0.74), residues: 41 loop : -0.75 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 493 HIS 0.003 0.001 HIS A 124 PHE 0.008 0.001 PHE A 265 TYR 0.015 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 56 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9368 (tp40) cc_final: 0.9098 (tm-30) REVERT: A 207 LYS cc_start: 0.7712 (tmmt) cc_final: 0.7213 (mttp) REVERT: A 242 ASP cc_start: 0.8991 (t70) cc_final: 0.8650 (t0) outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 2.2189 time to fit residues: 122.1917 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 : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 157 MET 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: 0.1980 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.092593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.072739 restraints weight = 20737.813| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.80 r_work: 0.2949 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 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 = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3774 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= 0.166 Angle : 0.534 4.717 5393 Z= 0.263 Chirality : 0.038 0.123 586 Planarity : 0.005 0.062 700 Dihedral : 3.744 15.488 535 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.48 % Allowed : 14.83 % 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: 0.65 (0.38), residues: 495 helix: 2.01 (0.37), residues: 220 sheet: -1.82 (0.76), residues: 41 loop : -0.67 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 493 HIS 0.003 0.001 HIS A 124 PHE 0.009 0.001 PHE A 487 TYR 0.011 0.001 TYR A 455 ARG 0.009 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 53 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9363 (tp40) cc_final: 0.9094 (tm-30) REVERT: A 207 LYS cc_start: 0.7670 (tmmt) cc_final: 0.7169 (mttp) REVERT: A 242 ASP cc_start: 0.8969 (t70) cc_final: 0.8639 (t0) REVERT: A 344 ASP cc_start: 0.8831 (m-30) cc_final: 0.8262 (m-30) outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 2.2333 time to fit residues: 123.1021 Evaluate side-chains 48 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 459 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.092820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.073190 restraints weight = 20992.473| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.77 r_work: 0.2955 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 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 = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3785 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= 0.183 Angle : 0.533 4.545 5393 Z= 0.263 Chirality : 0.038 0.124 586 Planarity : 0.005 0.065 700 Dihedral : 3.703 15.296 535 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.72 % Allowed : 14.83 % Favored : 84.45 % 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: 0.62 (0.38), residues: 495 helix: 2.01 (0.37), residues: 220 sheet: -1.89 (0.75), residues: 44 loop : -0.68 (0.37), residues: 231 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 0.016 0.001 TYR A 455 ARG 0.007 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: 3 poor density : 51 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.8766 (mp10) cc_final: 0.8542 (pm20) REVERT: A 96 GLN cc_start: 0.9357 (tp40) cc_final: 0.9098 (tm-30) REVERT: A 207 LYS cc_start: 0.7698 (tmmt) cc_final: 0.7190 (mttp) REVERT: A 242 ASP cc_start: 0.9003 (t70) cc_final: 0.8674 (t0) REVERT: A 344 ASP cc_start: 0.8846 (m-30) cc_final: 0.8284 (m-30) outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 2.2532 time to fit residues: 126.3221 Evaluate side-chains 51 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 459 SER 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: 1.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.093630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.074119 restraints weight = 20658.230| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.77 r_work: 0.2954 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 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 = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3968 Z= 0.154 Angle : 0.531 4.920 5393 Z= 0.261 Chirality : 0.038 0.123 586 Planarity : 0.006 0.085 700 Dihedral : 3.673 15.357 535 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.96 % Allowed : 15.07 % 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: 0.71 (0.38), residues: 495 helix: 2.10 (0.37), residues: 220 sheet: -1.74 (0.78), residues: 43 loop : -0.69 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 493 HIS 0.002 0.001 HIS A 124 PHE 0.013 0.001 PHE A 487 TYR 0.016 0.001 TYR A 455 ARG 0.011 0.001 ARG A 397 ********************** 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 54 residues out of total 429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.9359 (tp40) cc_final: 0.9094 (tm-30) REVERT: A 207 LYS cc_start: 0.7673 (tmmt) cc_final: 0.7177 (mttp) REVERT: A 242 ASP cc_start: 0.9008 (t70) cc_final: 0.8679 (t0) REVERT: A 344 ASP cc_start: 0.8810 (m-30) cc_final: 0.8236 (m-30) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 2.0378 time to fit residues: 112.5638 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 : 0.559 ------------------------------------------------------------------------------- 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 459 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.0022 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.092997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.073370 restraints weight = 20501.036| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.72 r_work: 0.2977 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 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 = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3968 Z= 0.192 Angle : 0.544 5.545 5393 Z= 0.270 Chirality : 0.038 0.123 586 Planarity : 0.006 0.074 700 Dihedral : 3.692 15.158 535 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.72 % Allowed : 15.79 % 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: 0.65 (0.38), residues: 495 helix: 2.09 (0.37), residues: 220 sheet: -1.84 (0.76), residues: 44 loop : -0.74 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 493 HIS 0.003 0.001 HIS A 124 PHE 0.008 0.001 PHE A 265 TYR 0.017 0.001 TYR A 455 ARG 0.010 0.001 ARG A 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6706.24 seconds wall clock time: 114 minutes 8.04 seconds (6848.04 seconds total)