Starting phenix.real_space_refine on Sat Apr 26 23:32:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzu_36753/04_2025/8jzu_36753.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzu_36753/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jzu_36753/04_2025/8jzu_36753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzu_36753/04_2025/8jzu_36753.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzu_36753/04_2025/8jzu_36753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzu_36753/04_2025/8jzu_36753.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 3.06, per 1000 atoms: 0.82 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: 0.88 Conformation dependent library (CDL) restraints added in 417.8 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: 0.41 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: 1.04 Time building geometry restraints manager: 1.06 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: 1.960 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.780 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.007 0.001 TRP A 453 HIS 0.003 0.001 HIS A 348 PHE 0.016 0.001 PHE A 195 TYR 0.035 0.002 TYR A 199 ARG 0.001 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 1) link_NAG-ASN : angle 10.03650 ( 3) hydrogen bonds : bond 0.08364 ( 277) hydrogen bonds : angle 4.55762 ( 822) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.21516 ( 2) covalent geometry : bond 0.00352 ( 3831) covalent geometry : angle 0.58748 ( 5204) *********************** 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 : 0.370 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: 0.2000 time to fit residues: 31.2787 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 : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.0010 chunk 36 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.4144 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.199491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.176308 restraints weight = 4610.908| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 1.92 r_work: 0.4049 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3833 Z= 0.139 Angle : 0.560 6.048 5209 Z= 0.281 Chirality : 0.039 0.161 610 Planarity : 0.004 0.048 638 Dihedral : 3.957 16.788 537 Min Nonbonded Distance : 2.456 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.40), residues: 476 helix: 2.13 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.38 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 517 HIS 0.006 0.002 HIS A 303 PHE 0.011 0.001 PHE A 198 TYR 0.021 0.002 TYR A 335 ARG 0.005 0.001 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00049 ( 1) link_NAG-ASN : angle 3.19794 ( 3) hydrogen bonds : bond 0.03827 ( 277) hydrogen bonds : angle 3.97202 ( 822) SS BOND : bond 0.00196 ( 1) SS BOND : angle 0.39555 ( 2) covalent geometry : bond 0.00287 ( 3831) covalent geometry : angle 0.55478 ( 5204) *********************** 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 : 0.405 Fit side-chains REVERT: A 172 LYS cc_start: 0.7811 (ttpp) cc_final: 0.7255 (ttmt) REVERT: A 321 ILE cc_start: 0.8605 (mt) cc_final: 0.8327 (mt) outliers start: 6 outliers final: 2 residues processed: 90 average time/residue: 0.1234 time to fit residues: 14.4687 Evaluate side-chains 77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN A 457 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.191283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.167485 restraints weight = 4617.428| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.92 r_work: 0.3940 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3833 Z= 0.168 Angle : 0.576 8.692 5209 Z= 0.288 Chirality : 0.038 0.160 610 Planarity : 0.004 0.048 638 Dihedral : 3.958 17.345 537 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.32 % Allowed : 16.24 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.39), residues: 476 helix: 1.83 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.36 (0.59), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 368 HIS 0.005 0.002 HIS A 348 PHE 0.017 0.002 PHE A 198 TYR 0.025 0.002 TYR A 342 ARG 0.003 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00012 ( 1) link_NAG-ASN : angle 2.88406 ( 3) hydrogen bonds : bond 0.03951 ( 277) hydrogen bonds : angle 4.11271 ( 822) SS BOND : bond 0.00711 ( 1) SS BOND : angle 0.32631 ( 2) covalent geometry : bond 0.00387 ( 3831) covalent geometry : angle 0.57253 ( 5204) *********************** 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: 9 poor density : 83 time to evaluate : 0.391 Fit side-chains REVERT: A 465 GLU cc_start: 0.7659 (tt0) cc_final: 0.7396 (tt0) outliers start: 9 outliers final: 5 residues processed: 89 average time/residue: 0.1093 time to fit residues: 13.0854 Evaluate side-chains 77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 37 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 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 63 ASN A 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.188389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.164101 restraints weight = 4630.445| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.92 r_work: 0.3906 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3624 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= 0.162 Angle : 0.561 7.425 5209 Z= 0.282 Chirality : 0.039 0.155 610 Planarity : 0.004 0.047 638 Dihedral : 3.888 19.374 537 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.58 % Allowed : 15.98 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.39), residues: 476 helix: 1.75 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.20 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.004 0.001 HIS A 348 PHE 0.024 0.002 PHE A 194 TYR 0.028 0.002 TYR A 342 ARG 0.003 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 1) link_NAG-ASN : angle 2.57628 ( 3) hydrogen bonds : bond 0.03924 ( 277) hydrogen bonds : angle 4.17707 ( 822) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.26050 ( 2) covalent geometry : bond 0.00378 ( 3831) covalent geometry : angle 0.55801 ( 5204) *********************** 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 : 0.408 Fit side-chains REVERT: A 335 TYR cc_start: 0.8146 (t80) cc_final: 0.7865 (t80) REVERT: A 413 MET cc_start: 0.7003 (ttm) cc_final: 0.6648 (ttm) REVERT: A 465 GLU cc_start: 0.7726 (tt0) cc_final: 0.7493 (tt0) outliers start: 10 outliers final: 7 residues processed: 79 average time/residue: 0.1150 time to fit residues: 12.2534 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 : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 2 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 526 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.185512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.160976 restraints weight = 4752.170| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.94 r_work: 0.3868 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4052 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= 0.170 Angle : 0.566 6.675 5209 Z= 0.286 Chirality : 0.039 0.151 610 Planarity : 0.004 0.046 638 Dihedral : 3.984 23.733 537 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.61 % Allowed : 15.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.39), residues: 476 helix: 1.62 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.42 (0.59), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.004 0.001 HIS A 348 PHE 0.016 0.002 PHE A 195 TYR 0.030 0.003 TYR A 342 ARG 0.003 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 1) link_NAG-ASN : angle 2.49627 ( 3) hydrogen bonds : bond 0.03992 ( 277) hydrogen bonds : angle 4.27678 ( 822) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.12433 ( 2) covalent geometry : bond 0.00395 ( 3831) covalent geometry : angle 0.56260 ( 5204) *********************** 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 84 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 SER cc_start: 0.7557 (p) cc_final: 0.7172 (t) REVERT: A 413 MET cc_start: 0.7037 (ttm) cc_final: 0.6741 (ttm) REVERT: A 465 GLU cc_start: 0.7618 (tt0) cc_final: 0.7210 (tt0) outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.1183 time to fit residues: 12.4437 Evaluate side-chains 77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 221 SER 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 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.184938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.160097 restraints weight = 4769.331| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.96 r_work: 0.3866 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4144 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= 0.157 Angle : 0.562 6.657 5209 Z= 0.283 Chirality : 0.038 0.146 610 Planarity : 0.004 0.046 638 Dihedral : 3.930 19.440 537 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.32 % Allowed : 18.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.38), residues: 476 helix: 1.62 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.48 (0.58), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.004 0.001 HIS A 362 PHE 0.014 0.001 PHE A 195 TYR 0.020 0.002 TYR A 342 ARG 0.002 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 1) link_NAG-ASN : angle 2.41554 ( 3) hydrogen bonds : bond 0.03949 ( 277) hydrogen bonds : angle 4.29589 ( 822) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.06964 ( 2) covalent geometry : bond 0.00364 ( 3831) covalent geometry : angle 0.55964 ( 5204) *********************** 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 77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8444 (tt) REVERT: A 320 LYS cc_start: 0.8329 (mmmt) cc_final: 0.7760 (mtpp) REVERT: A 321 ILE cc_start: 0.8893 (mp) cc_final: 0.8686 (mp) REVERT: A 465 GLU cc_start: 0.7643 (tt0) cc_final: 0.7173 (tt0) outliers start: 9 outliers final: 8 residues processed: 74 average time/residue: 0.1214 time to fit residues: 12.0986 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 : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 223 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.184578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.160348 restraints weight = 4704.199| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.91 r_work: 0.3865 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3833 Z= 0.150 Angle : 0.549 6.675 5209 Z= 0.276 Chirality : 0.037 0.141 610 Planarity : 0.004 0.046 638 Dihedral : 3.881 14.834 537 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.35 % Allowed : 17.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.38), residues: 476 helix: 1.62 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.52 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 PHE 0.014 0.001 PHE A 195 TYR 0.020 0.002 TYR A 342 ARG 0.002 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 1) link_NAG-ASN : angle 2.28216 ( 3) hydrogen bonds : bond 0.03860 ( 277) hydrogen bonds : angle 4.29294 ( 822) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.06235 ( 2) covalent geometry : bond 0.00346 ( 3831) covalent geometry : angle 0.54612 ( 5204) *********************** 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 82 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8420 (tt) REVERT: A 320 LYS cc_start: 0.8253 (mmmt) cc_final: 0.7694 (mtpp) REVERT: A 321 ILE cc_start: 0.8856 (mt) cc_final: 0.8633 (mp) REVERT: A 400 SER cc_start: 0.7575 (p) cc_final: 0.7206 (t) REVERT: A 465 GLU cc_start: 0.7583 (tt0) cc_final: 0.7290 (tt0) REVERT: A 526 ASN cc_start: 0.6431 (OUTLIER) cc_final: 0.6031 (t0) outliers start: 13 outliers final: 9 residues processed: 78 average time/residue: 0.1142 time to fit residues: 11.9341 Evaluate side-chains 75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 221 SER Chi-restraints excluded: chain A residue 223 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.183942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.159730 restraints weight = 4708.093| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.91 r_work: 0.3858 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3833 Z= 0.158 Angle : 0.557 6.700 5209 Z= 0.280 Chirality : 0.038 0.143 610 Planarity : 0.004 0.046 638 Dihedral : 3.924 18.856 537 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.38), residues: 476 helix: 1.62 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.55 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 PHE 0.014 0.001 PHE A 195 TYR 0.018 0.002 TYR A 342 ARG 0.002 0.000 ARG A 426 Details of bonding type rmsd link_NAG-ASN : bond 0.00096 ( 1) link_NAG-ASN : angle 2.22650 ( 3) hydrogen bonds : bond 0.03878 ( 277) hydrogen bonds : angle 4.31062 ( 822) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.07920 ( 2) covalent geometry : bond 0.00369 ( 3831) covalent geometry : angle 0.55437 ( 5204) *********************** 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 80 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8416 (tt) REVERT: A 320 LYS cc_start: 0.8226 (mmmt) cc_final: 0.7709 (mtpp) REVERT: A 321 ILE cc_start: 0.8865 (mt) cc_final: 0.8640 (mp) REVERT: A 400 SER cc_start: 0.7576 (p) cc_final: 0.7206 (t) REVERT: A 465 GLU cc_start: 0.7586 (tt0) cc_final: 0.7372 (tt0) outliers start: 13 outliers final: 10 residues processed: 76 average time/residue: 0.1204 time to fit residues: 12.1540 Evaluate side-chains 75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 118 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 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 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 = 0.4233 r_free = 0.4233 target = 0.183856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.159546 restraints weight = 4629.425| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.89 r_work: 0.3855 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 0.053 3833 Z= 0.154 Angle : 0.554 6.726 5209 Z= 0.280 Chirality : 0.038 0.143 610 Planarity : 0.004 0.046 638 Dihedral : 4.016 25.063 537 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.87 % Allowed : 16.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.38), residues: 476 helix: 1.62 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.62 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 PHE 0.014 0.001 PHE A 195 TYR 0.019 0.002 TYR A 342 ARG 0.002 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 1) link_NAG-ASN : angle 2.13493 ( 3) hydrogen bonds : bond 0.03844 ( 277) hydrogen bonds : angle 4.31047 ( 822) SS BOND : bond 0.00016 ( 1) SS BOND : angle 0.13808 ( 2) covalent geometry : bond 0.00358 ( 3831) covalent geometry : angle 0.55216 ( 5204) *********************** 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 83 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8486 (tt) REVERT: A 321 ILE cc_start: 0.8854 (mt) cc_final: 0.8629 (mp) REVERT: A 400 SER cc_start: 0.7581 (p) cc_final: 0.7214 (t) REVERT: A 465 GLU cc_start: 0.7595 (tt0) cc_final: 0.7291 (tt0) outliers start: 15 outliers final: 12 residues processed: 78 average time/residue: 0.1242 time to fit residues: 12.7545 Evaluate side-chains 77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 183 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.184730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.160329 restraints weight = 4695.215| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.92 r_work: 0.3864 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3833 Z= 0.142 Angle : 0.568 7.587 5209 Z= 0.286 Chirality : 0.038 0.143 610 Planarity : 0.004 0.046 638 Dihedral : 3.911 19.483 537 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.38), residues: 476 helix: 1.69 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.62 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 PHE 0.013 0.001 PHE A 198 TYR 0.015 0.002 TYR A 342 ARG 0.002 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 1) link_NAG-ASN : angle 2.04523 ( 3) hydrogen bonds : bond 0.03721 ( 277) hydrogen bonds : angle 4.25381 ( 822) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.16949 ( 2) covalent geometry : bond 0.00328 ( 3831) covalent geometry : angle 0.56638 ( 5204) ********************** 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 81 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8507 (tt) REVERT: A 320 LYS cc_start: 0.8326 (mmmt) cc_final: 0.7808 (mtpp) REVERT: A 321 ILE cc_start: 0.8821 (mt) cc_final: 0.8618 (mp) REVERT: A 400 SER cc_start: 0.7536 (p) cc_final: 0.7175 (t) REVERT: A 465 GLU cc_start: 0.7490 (tt0) cc_final: 0.7123 (tt0) outliers start: 12 outliers final: 10 residues processed: 76 average time/residue: 0.1266 time to fit residues: 12.6714 Evaluate side-chains 77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 118 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.184875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.160635 restraints weight = 4642.338| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 1.89 r_work: 0.3869 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3833 Z= 0.144 Angle : 0.561 6.706 5209 Z= 0.282 Chirality : 0.038 0.143 610 Planarity : 0.004 0.046 638 Dihedral : 3.878 17.037 537 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.38), residues: 476 helix: 1.74 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -1.60 (0.56), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 PHE 0.016 0.001 PHE A 195 TYR 0.016 0.002 TYR A 335 ARG 0.002 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 1) link_NAG-ASN : angle 1.97996 ( 3) hydrogen bonds : bond 0.03721 ( 277) hydrogen bonds : angle 4.24584 ( 822) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.18230 ( 2) covalent geometry : bond 0.00336 ( 3831) covalent geometry : angle 0.55964 ( 5204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2369.44 seconds wall clock time: 41 minutes 38.67 seconds (2498.67 seconds total)