Starting phenix.real_space_refine on Fri Aug 22 14:06:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzu_36753/08_2025/8jzu_36753.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzu_36753/08_2025/8jzu_36753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jzu_36753/08_2025/8jzu_36753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzu_36753/08_2025/8jzu_36753.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jzu_36753/08_2025/8jzu_36753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzu_36753/08_2025/8jzu_36753.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.002 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2474 2.51 5 N 599 2.21 5 O 646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3741 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3620 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 107 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.25, per 1000 atoms: 0.33 Number of scatterers: 3741 At special positions: 0 Unit cell: (80.1135, 67.464, 73.3671, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 646 8.00 N 599 7.00 C 2474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 436 " Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 158.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 890 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 80.1% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 33 through 57 removed outlier: 4.103A pdb=" N ALA A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 70 through 99 removed outlier: 4.196A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix removed outlier: 3.637A pdb=" N ARG A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 125 Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 125 through 134 removed outlier: 4.109A pdb=" N ALA A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 184 removed outlier: 3.580A pdb=" N LEU A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.777A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 220 removed outlier: 4.162A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 243 removed outlier: 3.727A pdb=" N GLY A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Proline residue: A 229 - end of helix Processing helix chain 'A' and resid 255 through 267 removed outlier: 4.399A pdb=" N ASP A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 337 Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 367 through 396 Proline residue: A 382 - end of helix removed outlier: 4.852A pdb=" N ASP A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix Processing helix chain 'A' and resid 400 through 430 Processing helix chain 'A' and resid 450 through 453 removed outlier: 3.665A pdb=" N TRP A 453 " --> pdb=" O SER A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 454 through 479 removed outlier: 3.577A pdb=" N TYR A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 473 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 511 Processing helix chain 'A' and resid 531 through 558 removed outlier: 3.901A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 556 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 9 through 13 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 439 removed outlier: 4.083A pdb=" N VAL A 442 " --> pdb=" O ILE A 439 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 822 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: 0.62 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1121 1.34 - 1.46: 598 1.46 - 1.57: 2078 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 3831 Sorted by residual: bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.427 -0.024 2.00e-02 2.50e+03 1.50e+00 bond pdb=" CB ASN A 203 " pdb=" CG ASN A 203 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.46e+00 bond pdb=" C6 NAG A 601 " pdb=" O6 NAG A 601 " ideal model delta sigma weight residual 1.408 1.432 -0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C4 NAG A 601 " pdb=" O4 NAG A 601 " ideal model delta sigma weight residual 1.409 1.430 -0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" CG1 ILE A 466 " pdb=" CD1 ILE A 466 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.04e+00 ... (remaining 3826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 4996 1.22 - 2.45: 152 2.45 - 3.67: 32 3.67 - 4.90: 15 4.90 - 6.12: 9 Bond angle restraints: 5204 Sorted by residual: angle pdb=" N GLY A 64 " pdb=" CA GLY A 64 " pdb=" C GLY A 64 " ideal model delta sigma weight residual 111.20 115.12 -3.92 1.39e+00 5.18e-01 7.97e+00 angle pdb=" CA TYR A 199 " pdb=" CB TYR A 199 " pdb=" CG TYR A 199 " ideal model delta sigma weight residual 113.90 118.35 -4.45 1.80e+00 3.09e-01 6.11e+00 angle pdb=" N VAL A 322 " pdb=" CA VAL A 322 " pdb=" C VAL A 322 " ideal model delta sigma weight residual 108.88 114.19 -5.31 2.16e+00 2.14e-01 6.05e+00 angle pdb=" C LEU A 379 " pdb=" N LEU A 380 " pdb=" CA LEU A 380 " ideal model delta sigma weight residual 122.36 118.16 4.20 1.72e+00 3.38e-01 5.96e+00 angle pdb=" C GLN A 485 " pdb=" N SER A 486 " pdb=" CA SER A 486 " ideal model delta sigma weight residual 121.54 126.07 -4.53 1.91e+00 2.74e-01 5.63e+00 ... (remaining 5199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 2005 17.22 - 34.44: 186 34.44 - 51.65: 35 51.65 - 68.87: 4 68.87 - 86.09: 2 Dihedral angle restraints: 2232 sinusoidal: 842 harmonic: 1390 Sorted by residual: dihedral pdb=" CG ARG A 192 " pdb=" CD ARG A 192 " pdb=" NE ARG A 192 " pdb=" CZ ARG A 192 " ideal model delta sinusoidal sigma weight residual 180.00 135.39 44.61 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU B 4 " pdb=" CG GLU B 4 " pdb=" CD GLU B 4 " pdb=" OE1 GLU B 4 " ideal model delta sinusoidal sigma weight residual 0.00 -86.09 86.09 1 3.00e+01 1.11e-03 9.94e+00 dihedral pdb=" CG LYS A 403 " pdb=" CD LYS A 403 " pdb=" CE LYS A 403 " pdb=" NZ LYS A 403 " ideal model delta sinusoidal sigma weight residual -180.00 -127.04 -52.96 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 2229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 412 0.034 - 0.068: 140 0.068 - 0.102: 42 0.102 - 0.136: 12 0.136 - 0.169: 4 Chirality restraints: 610 Sorted by residual: chirality pdb=" CA THR A 176 " pdb=" N THR A 176 " pdb=" C THR A 176 " pdb=" CB THR A 176 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 436 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CB VAL A 183 " pdb=" CA VAL A 183 " pdb=" CG1 VAL A 183 " pdb=" CG2 VAL A 183 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 607 not shown) Planarity restraints: 639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 436 " 0.019 2.00e-02 2.50e+03 2.28e-02 6.50e+00 pdb=" CG ASN A 436 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN A 436 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 436 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 199 " -0.011 2.00e-02 2.50e+03 1.42e-02 4.04e+00 pdb=" CG TYR A 199 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 199 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 199 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 199 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 199 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 199 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 199 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 455 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO A 456 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " 0.026 5.00e-02 4.00e+02 ... (remaining 636 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 416 2.74 - 3.28: 3819 3.28 - 3.82: 6363 3.82 - 4.36: 7015 4.36 - 4.90: 12664 Nonbonded interactions: 30277 Sorted by model distance: nonbonded pdb=" O MET A 117 " pdb=" OG1 THR A 230 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR A 86 " pdb=" N MET B 1 " model vdw 2.266 3.120 nonbonded pdb=" OD1 ASN A 428 " pdb=" NZ LYS A 431 " model vdw 2.279 3.120 nonbonded pdb=" O LEU A 122 " pdb=" OG1 THR A 128 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR A 333 " pdb=" O GLY A 499 " model vdw 2.347 3.040 ... (remaining 30272 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 6.190 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3833 Z= 0.159 Angle : 0.635 14.675 5209 Z= 0.310 Chirality : 0.040 0.169 610 Planarity : 0.004 0.046 638 Dihedral : 13.672 86.091 1339 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.40), residues: 476 helix: 2.08 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -1.39 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 186 TYR 0.035 0.002 TYR A 199 PHE 0.016 0.001 PHE A 195 TRP 0.007 0.001 TRP A 453 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 3831) covalent geometry : angle 0.58748 ( 5204) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.21516 ( 2) hydrogen bonds : bond 0.08364 ( 277) hydrogen bonds : angle 4.55762 ( 822) link_NAG-ASN : bond 0.00100 ( 1) link_NAG-ASN : angle 10.03650 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.134 Fit side-chains REVERT: A 172 LYS cc_start: 0.7455 (ttpp) cc_final: 0.6745 (ttmt) REVERT: A 316 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7700 (mmtt) REVERT: A 321 ILE cc_start: 0.8318 (mt) cc_final: 0.8011 (mt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0887 time to fit residues: 13.8921 Evaluate side-chains 76 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.0050 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 244 GLN A 337 GLN A 454 GLN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.197395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.174017 restraints weight = 4657.372| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.92 r_work: 0.4016 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3833 Z= 0.146 Angle : 0.574 6.065 5209 Z= 0.289 Chirality : 0.039 0.162 610 Planarity : 0.004 0.049 638 Dihedral : 3.984 16.947 537 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.55 % Allowed : 10.57 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.40), residues: 476 helix: 2.08 (0.27), residues: 364 sheet: None (None), residues: 0 loop : -1.46 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 350 TYR 0.027 0.002 TYR A 335 PHE 0.011 0.001 PHE A 198 TRP 0.005 0.001 TRP A 368 HIS 0.006 0.002 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3831) covalent geometry : angle 0.56940 ( 5204) SS BOND : bond 0.00187 ( 1) SS BOND : angle 0.36450 ( 2) hydrogen bonds : bond 0.03901 ( 277) hydrogen bonds : angle 4.01180 ( 822) link_NAG-ASN : bond 0.00197 ( 1) link_NAG-ASN : angle 3.17766 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.185 Fit side-chains REVERT: A 172 LYS cc_start: 0.7782 (ttpp) cc_final: 0.7237 (ttmt) REVERT: A 321 ILE cc_start: 0.8624 (mt) cc_final: 0.8348 (mt) outliers start: 6 outliers final: 2 residues processed: 90 average time/residue: 0.0473 time to fit residues: 5.6207 Evaluate side-chains 73 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 370 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 22 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 196 ASN A 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.192557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.168918 restraints weight = 4596.963| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 1.90 r_work: 0.3947 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3833 Z= 0.158 Angle : 0.569 8.419 5209 Z= 0.282 Chirality : 0.038 0.159 610 Planarity : 0.004 0.048 638 Dihedral : 3.927 17.271 537 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.32 % Allowed : 16.49 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.39), residues: 476 helix: 1.86 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.35 (0.60), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 350 TYR 0.023 0.002 TYR A 342 PHE 0.016 0.002 PHE A 198 TRP 0.005 0.001 TRP A 69 HIS 0.004 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 3831) covalent geometry : angle 0.56495 ( 5204) SS BOND : bond 0.00186 ( 1) SS BOND : angle 0.25505 ( 2) hydrogen bonds : bond 0.03884 ( 277) hydrogen bonds : angle 4.08737 ( 822) link_NAG-ASN : bond 0.00056 ( 1) link_NAG-ASN : angle 2.92243 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.086 Fit side-chains REVERT: A 465 GLU cc_start: 0.7630 (tt0) cc_final: 0.7403 (tt0) outliers start: 9 outliers final: 5 residues processed: 85 average time/residue: 0.0449 time to fit residues: 5.1348 Evaluate side-chains 75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 549 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.0570 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.191055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.166999 restraints weight = 4617.349| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 1.91 r_work: 0.3933 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3833 Z= 0.137 Angle : 0.539 6.585 5209 Z= 0.270 Chirality : 0.037 0.153 610 Planarity : 0.004 0.047 638 Dihedral : 3.830 18.339 537 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.58 % Allowed : 17.01 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.39), residues: 476 helix: 1.88 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.21 (0.60), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 350 TYR 0.021 0.002 TYR A 342 PHE 0.023 0.001 PHE A 194 TRP 0.005 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3831) covalent geometry : angle 0.53514 ( 5204) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.15685 ( 2) hydrogen bonds : bond 0.03729 ( 277) hydrogen bonds : angle 4.06894 ( 822) link_NAG-ASN : bond 0.00080 ( 1) link_NAG-ASN : angle 2.65004 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.129 Fit side-chains REVERT: A 413 MET cc_start: 0.6624 (ttm) cc_final: 0.6278 (ttm) REVERT: A 465 GLU cc_start: 0.7695 (tt0) cc_final: 0.7324 (tt0) outliers start: 10 outliers final: 8 residues processed: 79 average time/residue: 0.0425 time to fit residues: 4.6255 Evaluate side-chains 74 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 2 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.187104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.162444 restraints weight = 4686.064| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.93 r_work: 0.3882 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3833 Z= 0.162 Angle : 0.560 6.698 5209 Z= 0.282 Chirality : 0.038 0.147 610 Planarity : 0.004 0.048 638 Dihedral : 3.907 22.470 537 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.09 % Allowed : 16.24 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.39), residues: 476 helix: 1.65 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.34 (0.60), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 350 TYR 0.027 0.002 TYR A 342 PHE 0.016 0.002 PHE A 120 TRP 0.006 0.001 TRP A 69 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3831) covalent geometry : angle 0.55741 ( 5204) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.14549 ( 2) hydrogen bonds : bond 0.03905 ( 277) hydrogen bonds : angle 4.19940 ( 822) link_NAG-ASN : bond 0.00131 ( 1) link_NAG-ASN : angle 2.46587 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.8185 (mmm) cc_final: 0.7866 (mmt) REVERT: A 413 MET cc_start: 0.6871 (ttm) cc_final: 0.6523 (ttm) REVERT: A 465 GLU cc_start: 0.7620 (tt0) cc_final: 0.7221 (tt0) outliers start: 12 outliers final: 8 residues processed: 79 average time/residue: 0.0416 time to fit residues: 4.5158 Evaluate side-chains 74 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.186070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.161651 restraints weight = 4710.413| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.93 r_work: 0.3877 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3833 Z= 0.151 Angle : 0.547 6.389 5209 Z= 0.276 Chirality : 0.037 0.146 610 Planarity : 0.004 0.047 638 Dihedral : 3.855 17.094 537 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.09 % Allowed : 16.75 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.38), residues: 476 helix: 1.67 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.35 (0.59), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 350 TYR 0.021 0.002 TYR A 342 PHE 0.017 0.001 PHE A 195 TRP 0.006 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3831) covalent geometry : angle 0.54385 ( 5204) SS BOND : bond 0.00079 ( 1) SS BOND : angle 0.08553 ( 2) hydrogen bonds : bond 0.03839 ( 277) hydrogen bonds : angle 4.21273 ( 822) link_NAG-ASN : bond 0.00115 ( 1) link_NAG-ASN : angle 2.37868 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8437 (tt) REVERT: A 117 MET cc_start: 0.8211 (mmm) cc_final: 0.7950 (mmt) REVERT: A 331 TYR cc_start: 0.8055 (t80) cc_final: 0.7851 (t80) REVERT: A 400 SER cc_start: 0.7543 (p) cc_final: 0.7167 (t) REVERT: A 413 MET cc_start: 0.6956 (ttm) cc_final: 0.6658 (ttm) REVERT: A 465 GLU cc_start: 0.7641 (tt0) cc_final: 0.7193 (tt0) REVERT: A 526 ASN cc_start: 0.6487 (OUTLIER) cc_final: 0.6117 (t0) outliers start: 12 outliers final: 9 residues processed: 78 average time/residue: 0.0438 time to fit residues: 4.7038 Evaluate side-chains 80 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 0.0670 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.186870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.162630 restraints weight = 4762.918| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.94 r_work: 0.3881 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3833 Z= 0.137 Angle : 0.535 6.333 5209 Z= 0.269 Chirality : 0.037 0.144 610 Planarity : 0.004 0.046 638 Dihedral : 3.854 19.627 537 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.09 % Allowed : 17.27 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.39), residues: 476 helix: 1.73 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.32 (0.58), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 350 TYR 0.021 0.002 TYR B 6 PHE 0.014 0.001 PHE A 195 TRP 0.005 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3831) covalent geometry : angle 0.53233 ( 5204) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.03115 ( 2) hydrogen bonds : bond 0.03748 ( 277) hydrogen bonds : angle 4.20915 ( 822) link_NAG-ASN : bond 0.00108 ( 1) link_NAG-ASN : angle 2.30773 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8431 (tt) REVERT: A 321 ILE cc_start: 0.8837 (mp) cc_final: 0.8628 (mp) REVERT: A 400 SER cc_start: 0.7599 (p) cc_final: 0.7213 (t) REVERT: A 413 MET cc_start: 0.6955 (ttm) cc_final: 0.6653 (ttm) REVERT: A 465 GLU cc_start: 0.7597 (tt0) cc_final: 0.7195 (tt0) outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.0500 time to fit residues: 5.3885 Evaluate side-chains 80 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 504 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.0670 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.186775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.162606 restraints weight = 4722.283| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.95 r_work: 0.3893 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3833 Z= 0.131 Angle : 0.540 6.450 5209 Z= 0.270 Chirality : 0.037 0.143 610 Planarity : 0.004 0.046 638 Dihedral : 3.765 14.371 537 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.84 % Allowed : 17.78 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.38), residues: 476 helix: 1.78 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.34 (0.58), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 350 TYR 0.019 0.002 TYR B 6 PHE 0.013 0.001 PHE A 198 TRP 0.005 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3831) covalent geometry : angle 0.53738 ( 5204) SS BOND : bond 0.00001 ( 1) SS BOND : angle 0.05731 ( 2) hydrogen bonds : bond 0.03627 ( 277) hydrogen bonds : angle 4.16498 ( 822) link_NAG-ASN : bond 0.00095 ( 1) link_NAG-ASN : angle 2.17972 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8388 (tt) REVERT: A 320 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7678 (mttm) REVERT: A 400 SER cc_start: 0.7579 (p) cc_final: 0.7229 (t) REVERT: A 413 MET cc_start: 0.6939 (ttm) cc_final: 0.6638 (ttm) outliers start: 11 outliers final: 8 residues processed: 79 average time/residue: 0.0515 time to fit residues: 5.4403 Evaluate side-chains 80 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 504 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.184597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.159573 restraints weight = 4735.851| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.95 r_work: 0.3858 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3833 Z= 0.167 Angle : 0.575 6.453 5209 Z= 0.292 Chirality : 0.038 0.143 610 Planarity : 0.004 0.047 638 Dihedral : 3.921 22.288 537 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.35 % Allowed : 16.75 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.38), residues: 476 helix: 1.61 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.39 (0.58), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 426 TYR 0.042 0.002 TYR A 335 PHE 0.013 0.001 PHE A 195 TRP 0.006 0.001 TRP A 69 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 3831) covalent geometry : angle 0.57320 ( 5204) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.06488 ( 2) hydrogen bonds : bond 0.03900 ( 277) hydrogen bonds : angle 4.30451 ( 822) link_NAG-ASN : bond 0.00127 ( 1) link_NAG-ASN : angle 2.12198 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8497 (tt) REVERT: A 320 LYS cc_start: 0.8266 (mmmt) cc_final: 0.7664 (mtpp) REVERT: A 400 SER cc_start: 0.7576 (p) cc_final: 0.7213 (t) REVERT: A 413 MET cc_start: 0.7103 (ttm) cc_final: 0.6868 (ttm) outliers start: 13 outliers final: 11 residues processed: 81 average time/residue: 0.0441 time to fit residues: 4.9908 Evaluate side-chains 82 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 504 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 7 optimal weight: 0.0050 chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 526 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.185820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.161673 restraints weight = 4735.486| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.94 r_work: 0.3880 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3833 Z= 0.140 Angle : 0.559 6.010 5209 Z= 0.284 Chirality : 0.037 0.142 610 Planarity : 0.004 0.046 638 Dihedral : 3.806 16.193 537 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.09 % Allowed : 17.78 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.38), residues: 476 helix: 1.77 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -1.51 (0.56), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 350 TYR 0.017 0.002 TYR B 6 PHE 0.014 0.001 PHE A 195 TRP 0.007 0.001 TRP A 69 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3831) covalent geometry : angle 0.55695 ( 5204) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.12021 ( 2) hydrogen bonds : bond 0.03741 ( 277) hydrogen bonds : angle 4.25108 ( 822) link_NAG-ASN : bond 0.00076 ( 1) link_NAG-ASN : angle 2.03996 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8459 (tt) REVERT: A 320 LYS cc_start: 0.8213 (mmmt) cc_final: 0.7619 (mtpp) REVERT: A 335 TYR cc_start: 0.8022 (t80) cc_final: 0.7739 (t80) REVERT: A 400 SER cc_start: 0.7539 (p) cc_final: 0.7178 (t) REVERT: A 413 MET cc_start: 0.7094 (ttm) cc_final: 0.6849 (ttm) REVERT: A 526 ASN cc_start: 0.6456 (OUTLIER) cc_final: 0.6038 (t0) outliers start: 12 outliers final: 9 residues processed: 83 average time/residue: 0.0542 time to fit residues: 5.9492 Evaluate side-chains 82 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.0370 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.0060 chunk 12 optimal weight: 0.7980 overall best weight: 0.5274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.185922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.161818 restraints weight = 4610.486| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.93 r_work: 0.3880 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 3833 Z= 0.212 Angle : 1.214 59.198 5209 Z= 0.726 Chirality : 0.042 0.464 610 Planarity : 0.004 0.046 638 Dihedral : 3.907 21.747 537 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.35 % Allowed : 17.27 % Favored : 79.38 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.38), residues: 476 helix: 1.77 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -1.48 (0.56), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 151 TYR 0.015 0.002 TYR B 6 PHE 0.014 0.001 PHE A 194 TRP 0.006 0.001 TRP A 69 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 3831) covalent geometry : angle 1.21387 ( 5204) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.12519 ( 2) hydrogen bonds : bond 0.03766 ( 277) hydrogen bonds : angle 4.24987 ( 822) link_NAG-ASN : bond 0.00078 ( 1) link_NAG-ASN : angle 2.04010 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1125.12 seconds wall clock time: 20 minutes 2.27 seconds (1202.27 seconds total)