Starting phenix.real_space_refine on Wed Jul 1 22:56:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jzu_36753/07_2026/8jzu_36753.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzu_36753/07_2026/8jzu_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_36753/07_2026/8jzu_36753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzu_36753/07_2026/8jzu_36753.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jzu_36753/07_2026/8jzu_36753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzu_36753/07_2026/8jzu_36753.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jzu_36753/07_2026/8jzu_36753.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jzu_36753/07_2026/8jzu_36753.cif" } 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-dev-6108/lib/python3.11/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 chiralities: 1 Time building chain proxies: 0.99, per 1000 atoms: 0.26 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: 0.34 Conformation dependent library (CDL) restraints added in 146.3 milliseconds 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: 0.09 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: 0.43 Time building geometry restraints manager: 0.46 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: 1984 17.22 - 34.44: 186 34.44 - 51.65: 35 51.65 - 68.87: 4 68.87 - 86.09: 2 Dihedral angle restraints: 2211 sinusoidal: 821 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 2208 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: 2.180 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: 0.080 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.110 Find NCS groups from input model: 0.010 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 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 : 13.758 86.091 1318 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 are 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/Z covalent geometry : bond 0.00352 / 0.16 ( 3831) covalent geometry : angle 0.58748 / 0.30 ( 5204) SS BOND : bond 0.00011 / 0.01 ( 1) SS BOND : angle 0.21516 / 0.07 ( 2) hydrogen bonds : bond 0.08364 / 5.60 ( 277) hydrogen bonds : angle 4.55762 / 3.31 ( 822) link_NAG-ASN : bond 0.00100 / 0.06 ( 1) link_NAG-ASN : angle 10.03650 / 4.42 ( 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 : 0.147 Fit side-chains REVERT: A 172 LYS cc_start: 0.7455 (ttpp) cc_final: 0.6745 (ttmt) REVERT: A 316 LYS cc_start: 0.7943 (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: 0.0865 time to fit residues: 13.6778 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 : 0.132 ------------------------------------------------------------------------------- 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... A 219 ASN A 244 GLN A 337 GLN A 454 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.197823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.174401 restraints weight = 4665.275| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 1.93 r_work: 0.4026 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3833 Z= 0.145 Angle : 0.571 6.077 5209 Z= 0.288 Chirality : 0.039 0.161 610 Planarity : 0.004 0.048 638 Dihedral : 3.863 16.771 516 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.55 % Allowed : 10.82 % Favored : 87.63 % 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 are not related in a simple way. whole: 1.95 (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 0.004 0.001 ARG A 350 TYR 0.025 0.002 TYR A 335 PHE 0.011 0.001 PHE A 195 TRP 0.004 0.001 TRP A 368 HIS 0.006 0.002 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 3831) covalent geometry : angle 0.56616 / 0.29 ( 5204) SS BOND : bond 0.00169 / 0.11 ( 1) SS BOND : angle 0.27802 / 0.13 ( 2) hydrogen bonds : bond 0.03918 / 2.63 ( 277) hydrogen bonds : angle 4.01664 / 2.90 ( 822) link_NAG-ASN : bond 0.00196 / 0.12 ( 1) link_NAG-ASN : angle 3.20311 / 1.50 ( 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 : 0.135 Fit side-chains REVERT: A 172 LYS cc_start: 0.7869 (ttpp) cc_final: 0.7053 (ttmt) REVERT: A 321 ILE cc_start: 0.8630 (mt) cc_final: 0.8356 (mt) outliers start: 6 outliers final: 2 residues processed: 90 average time/residue: 0.0511 time to fit residues: 6.1347 Evaluate side-chains 76 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.0670 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4306 r_free = 0.4306 target = 0.190847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.167088 restraints weight = 4588.746| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 1.89 r_work: 0.3922 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3833 Z= 0.178 Angle : 0.590 8.916 5209 Z= 0.294 Chirality : 0.039 0.160 610 Planarity : 0.004 0.049 638 Dihedral : 3.998 18.011 516 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.09 % Allowed : 15.98 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.39), residues: 476 helix: 1.77 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.36 (0.59), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 350 TYR 0.028 0.003 TYR A 342 PHE 0.016 0.002 PHE A 120 TRP 0.007 0.001 TRP A 368 HIS 0.006 0.002 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 3831) covalent geometry : angle 0.58653 / 0.29 ( 5204) SS BOND : bond 0.00355 / 0.22 ( 1) SS BOND : angle 0.17878 / 0.08 ( 2) hydrogen bonds : bond 0.04056 / 2.73 ( 277) hydrogen bonds : angle 4.16884 / 3.00 ( 822) link_NAG-ASN : bond 0.00239 / 0.15 ( 1) link_NAG-ASN : angle 2.85816 / 1.23 ( 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 92 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.134 Fit side-chains REVERT: A 335 TYR cc_start: 0.8167 (t80) cc_final: 0.7966 (t80) REVERT: A 465 GLU cc_start: 0.7680 (tt0) cc_final: 0.7248 (tt0) outliers start: 12 outliers final: 5 residues processed: 86 average time/residue: 0.0500 time to fit residues: 5.8254 Evaluate side-chains 73 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.080 ------------------------------------------------------------------------------- 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: 0.5980 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.0040 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.0470 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 0.0470 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 ASN A 457 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.192422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.168898 restraints weight = 4605.610| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 1.90 r_work: 0.3958 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3382 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= 0.123 Angle : 0.517 5.964 5209 Z= 0.257 Chirality : 0.037 0.151 610 Planarity : 0.004 0.046 638 Dihedral : 3.860 17.939 516 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.58 % Allowed : 18.30 % 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 are not related in a simple way. whole: 1.92 (0.39), residues: 476 helix: 2.00 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -1.32 (0.59), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 350 TYR 0.017 0.002 TYR B 6 PHE 0.022 0.001 PHE A 194 TRP 0.004 0.001 TRP A 69 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 3831) covalent geometry : angle 0.51383 / 0.26 ( 5204) SS BOND : bond 0.00110 / 0.07 ( 1) SS BOND : angle 0.07023 / 0.02 ( 2) hydrogen bonds : bond 0.03558 / 2.41 ( 277) hydrogen bonds : angle 4.01768 / 2.90 ( 822) link_NAG-ASN : bond 0.00008 / 0.01 ( 1) link_NAG-ASN : angle 2.52308 / 1.17 ( 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 84 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.132 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 80 average time/residue: 0.0390 time to fit residues: 4.3880 Evaluate side-chains 75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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: 1.9990 chunk 20 optimal weight: 0.0070 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.188172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.163989 restraints weight = 4680.652| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.94 r_work: 0.3901 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3833 Z= 0.156 Angle : 0.553 6.518 5209 Z= 0.278 Chirality : 0.038 0.150 610 Planarity : 0.004 0.047 638 Dihedral : 3.920 21.381 516 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.58 % Allowed : 18.04 % 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 are not related in a simple way. whole: 1.70 (0.39), residues: 476 helix: 1.80 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.24 (0.60), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 350 TYR 0.025 0.002 TYR A 342 PHE 0.016 0.002 PHE A 198 TRP 0.005 0.001 TRP A 69 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 3831) covalent geometry : angle 0.55065 / 0.28 ( 5204) SS BOND : bond 0.00123 / 0.08 ( 1) SS BOND : angle 0.14965 / 0.05 ( 2) hydrogen bonds : bond 0.03874 / 2.60 ( 277) hydrogen bonds : angle 4.15264 / 3.02 ( 822) link_NAG-ASN : bond 0.00162 / 0.10 ( 1) link_NAG-ASN : angle 2.37715 / 1.05 ( 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 78 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.133 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 75 average time/residue: 0.0337 time to fit residues: 3.7107 Evaluate side-chains 72 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 379 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 0.0170 chunk 41 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.188800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.164922 restraints weight = 4674.020| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 1.95 r_work: 0.3917 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3833 Z= 0.126 Angle : 0.523 6.164 5209 Z= 0.262 Chirality : 0.037 0.147 610 Planarity : 0.004 0.045 638 Dihedral : 3.843 16.585 516 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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 are not related in a simple way. whole: 1.76 (0.39), residues: 476 helix: 1.84 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.23 (0.59), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 350 TYR 0.022 0.002 TYR A 335 PHE 0.016 0.001 PHE A 195 TRP 0.004 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 3831) covalent geometry : angle 0.52021 / 0.26 ( 5204) SS BOND : bond 0.00044 / 0.03 ( 1) SS BOND : angle 0.00755 / 0.00 ( 2) hydrogen bonds : bond 0.03596 / 2.42 ( 277) hydrogen bonds : angle 4.10321 / 2.99 ( 822) link_NAG-ASN : bond 0.00087 / 0.05 ( 1) link_NAG-ASN : angle 2.31940 / 1.06 ( 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 80 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8408 (tt) REVERT: A 117 MET cc_start: 0.7967 (mmm) cc_final: 0.7735 (mmt) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 0.0437 time to fit residues: 4.6065 Evaluate side-chains 75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 504 SER 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: 0.9980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.186092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.161911 restraints weight = 4746.253| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.96 r_work: 0.3885 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3833 Z= 0.150 Angle : 0.548 6.783 5209 Z= 0.276 Chirality : 0.038 0.145 610 Planarity : 0.004 0.045 638 Dihedral : 3.941 21.302 516 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.84 % Allowed : 19.07 % Favored : 78.09 % 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 are not related in a simple way. whole: 1.58 (0.39), residues: 476 helix: 1.75 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.44 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.022 0.002 TYR A 342 PHE 0.015 0.001 PHE A 198 TRP 0.005 0.001 TRP A 69 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 3831) covalent geometry : angle 0.54523 / 0.28 ( 5204) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 0.08192 / 0.03 ( 2) hydrogen bonds : bond 0.03785 / 2.51 ( 277) hydrogen bonds : angle 4.20132 / 3.06 ( 822) link_NAG-ASN : bond 0.00132 / 0.08 ( 1) link_NAG-ASN : angle 2.21722 / 1.00 ( 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 81 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8448 (tt) REVERT: A 321 ILE cc_start: 0.8875 (mp) cc_final: 0.8602 (mp) REVERT: A 526 ASN cc_start: 0.6310 (OUTLIER) cc_final: 0.5902 (t0) outliers start: 11 outliers final: 7 residues processed: 78 average time/residue: 0.0498 time to fit residues: 5.1132 Evaluate side-chains 77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 339 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 379 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.0170 chunk 33 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.186194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.162231 restraints weight = 4728.495| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.95 r_work: 0.3890 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4311 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= 0.139 Angle : 0.547 6.335 5209 Z= 0.274 Chirality : 0.037 0.144 610 Planarity : 0.004 0.044 638 Dihedral : 3.853 15.605 516 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.61 % Allowed : 17.53 % Favored : 78.87 % 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 are not related in a simple way. whole: 1.63 (0.39), residues: 476 helix: 1.82 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -1.48 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 350 TYR 0.022 0.002 TYR A 335 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/Z covalent geometry : bond 0.00316 / 0.14 ( 3831) covalent geometry : angle 0.54434 / 0.27 ( 5204) SS BOND : bond 0.00028 / 0.02 ( 1) SS BOND : angle 0.02542 / 0.01 ( 2) hydrogen bonds : bond 0.03707 / 2.47 ( 277) hydrogen bonds : angle 4.17394 / 3.05 ( 822) link_NAG-ASN : bond 0.00098 / 0.06 ( 1) link_NAG-ASN : angle 2.16175 / 0.99 ( 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 85 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8421 (tt) REVERT: A 320 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7685 (mtpp) REVERT: A 321 ILE cc_start: 0.8926 (mp) cc_final: 0.8686 (mp) outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.0376 time to fit residues: 3.9893 Evaluate side-chains 79 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 221 SER 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 379 LEU Chi-restraints excluded: chain A residue 413 MET 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: 4.9990 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.184501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.160334 restraints weight = 4714.632| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.94 r_work: 0.3865 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3833 Z= 0.154 Angle : 0.558 6.432 5209 Z= 0.282 Chirality : 0.037 0.146 610 Planarity : 0.004 0.045 638 Dihedral : 3.941 21.444 516 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.09 % Allowed : 18.81 % Favored : 78.09 % 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 are not related in a simple way. whole: 1.53 (0.39), residues: 476 helix: 1.76 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -1.61 (0.56), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.021 0.002 TYR A 335 PHE 0.017 0.001 PHE A 194 TRP 0.006 0.001 TRP A 69 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 3831) covalent geometry : angle 0.55554 / 0.28 ( 5204) SS BOND : bond 0.00019 / 0.01 ( 1) SS BOND : angle 0.08135 / 0.04 ( 2) hydrogen bonds : bond 0.03838 / 2.56 ( 277) hydrogen bonds : angle 4.23995 / 3.10 ( 822) link_NAG-ASN : bond 0.00109 / 0.07 ( 1) link_NAG-ASN : angle 2.09081 / 0.96 ( 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 82 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8391 (tt) REVERT: A 320 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7703 (mtpp) REVERT: A 321 ILE cc_start: 0.8916 (mp) cc_final: 0.8682 (mp) REVERT: A 400 SER cc_start: 0.7597 (p) cc_final: 0.7238 (t) outliers start: 12 outliers final: 10 residues processed: 79 average time/residue: 0.0487 time to fit residues: 5.2001 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 : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 223 VAL 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 379 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: 1.9990 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.183304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.159049 restraints weight = 4745.191| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.95 r_work: 0.3849 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3833 Z= 0.162 Angle : 0.578 6.526 5209 Z= 0.292 Chirality : 0.038 0.144 610 Planarity : 0.004 0.045 638 Dihedral : 3.909 16.227 516 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.61 % Allowed : 18.04 % Favored : 78.35 % 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 are not related in a simple way. whole: 1.45 (0.38), residues: 476 helix: 1.68 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.58 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 426 TYR 0.022 0.002 TYR A 342 PHE 0.017 0.001 PHE A 194 TRP 0.007 0.001 TRP A 69 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 3831) covalent geometry : angle 0.57595 / 0.29 ( 5204) SS BOND : bond 0.00013 / 0.01 ( 1) SS BOND : angle 0.11846 / 0.05 ( 2) hydrogen bonds : bond 0.03897 / 2.60 ( 277) hydrogen bonds : angle 4.27321 / 3.13 ( 822) link_NAG-ASN : bond 0.00069 / 0.04 ( 1) link_NAG-ASN : angle 2.04440 / 0.95 ( 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 83 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8415 (tt) REVERT: A 320 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7725 (mtpp) REVERT: A 321 ILE cc_start: 0.8920 (mp) cc_final: 0.8682 (mp) REVERT: A 400 SER cc_start: 0.7567 (p) cc_final: 0.7210 (t) outliers start: 14 outliers final: 11 residues processed: 79 average time/residue: 0.0480 time to fit residues: 5.2188 Evaluate side-chains 80 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 223 VAL 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 379 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 34 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.183920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.159259 restraints weight = 4614.955| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.92 r_work: 0.3858 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4659 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= 0.155 Angle : 0.572 6.515 5209 Z= 0.289 Chirality : 0.038 0.144 610 Planarity : 0.004 0.045 638 Dihedral : 3.982 23.361 516 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.61 % Allowed : 17.78 % Favored : 78.61 % 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 are not related in a simple way. whole: 1.42 (0.38), residues: 476 helix: 1.65 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.55 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.021 0.002 TYR A 342 PHE 0.019 0.001 PHE A 194 TRP 0.007 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 3831) covalent geometry : angle 0.57074 / 0.29 ( 5204) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 0.17503 / 0.07 ( 2) hydrogen bonds : bond 0.03898 / 2.62 ( 277) hydrogen bonds : angle 4.27831 / 3.14 ( 822) link_NAG-ASN : bond 0.00057 / 0.04 ( 1) link_NAG-ASN : angle 1.99363 / 0.93 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1103.83 seconds wall clock time: 19 minutes 42.66 seconds (1182.66 seconds total)