Starting phenix.real_space_refine on Fri May 9 20:56:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzu_36753/05_2025/8jzu_36753.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzu_36753/05_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_36753/05_2025/8jzu_36753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzu_36753/05_2025/8jzu_36753.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzu_36753/05_2025/8jzu_36753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzu_36753/05_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-5687/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: 3.02, per 1000 atoms: 0.81 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: 0.84 Conformation dependent library (CDL) restraints added in 417.3 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: 0.29 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: 0.97 Time building geometry restraints manager: 1.00 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: 1.130 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.780 Find NCS groups from input model: 0.030 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- 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 : 0.371 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: 0.1933 time to fit residues: 30.3187 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 : 0.386 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 337 GLN A 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.200241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.177148 restraints weight = 4611.317| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.91 r_work: 0.4052 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3833 Z= 0.132 Angle : 0.558 6.059 5209 Z= 0.280 Chirality : 0.038 0.161 610 Planarity : 0.004 0.048 638 Dihedral : 3.949 16.819 537 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.03 % Allowed : 11.34 % 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: 2.06 (0.40), residues: 476 helix: 2.15 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.39 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 453 HIS 0.005 0.002 HIS A 303 PHE 0.012 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 0.00014 ( 1) link_NAG-ASN : angle 3.26023 ( 3) hydrogen bonds : bond 0.03825 ( 277) hydrogen bonds : angle 3.95785 ( 822) SS BOND : bond 0.00207 ( 1) SS BOND : angle 0.42608 ( 2) covalent geometry : bond 0.00285 ( 3831) covalent geometry : angle 0.55288 ( 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 91 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.420 Fit side-chains REVERT: A 172 LYS cc_start: 0.7794 (ttpp) cc_final: 0.7199 (ttmt) REVERT: A 321 ILE cc_start: 0.8604 (mt) cc_final: 0.8326 (mt) outliers start: 4 outliers final: 1 residues processed: 88 average time/residue: 0.1304 time to fit residues: 14.9686 Evaluate side-chains 77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 32 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 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 196 ASN 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 = 0.4302 r_free = 0.4302 target = 0.191048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.166930 restraints weight = 4620.839| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 1.93 r_work: 0.3934 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3149 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= 0.166 Angle : 0.562 6.011 5209 Z= 0.284 Chirality : 0.039 0.161 610 Planarity : 0.004 0.048 638 Dihedral : 3.937 17.749 537 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.58 % Allowed : 14.95 % Favored : 82.47 % 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: 1.68 (0.39), residues: 476 helix: 1.81 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.37 (0.58), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 368 HIS 0.005 0.001 HIS A 348 PHE 0.019 0.002 PHE A 195 TYR 0.028 0.003 TYR A 342 ARG 0.005 0.001 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00021 ( 1) link_NAG-ASN : angle 2.67050 ( 3) hydrogen bonds : bond 0.03908 ( 277) hydrogen bonds : angle 4.09409 ( 822) SS BOND : bond 0.00729 ( 1) SS BOND : angle 0.18148 ( 2) covalent geometry : bond 0.00376 ( 3831) covalent geometry : angle 0.55845 ( 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 91 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.373 Fit side-chains REVERT: A 335 TYR cc_start: 0.8146 (t80) cc_final: 0.7908 (t80) REVERT: A 465 GLU cc_start: 0.7638 (tt0) cc_final: 0.7298 (tt0) outliers start: 10 outliers final: 5 residues processed: 88 average time/residue: 0.1135 time to fit residues: 13.3217 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 : 0.413 ------------------------------------------------------------------------------- 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 519 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 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 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.186898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.162407 restraints weight = 4642.352| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.91 r_work: 0.3887 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3833 Z= 0.166 Angle : 0.563 6.899 5209 Z= 0.283 Chirality : 0.038 0.153 610 Planarity : 0.004 0.047 638 Dihedral : 3.925 19.396 537 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: 1.61 (0.39), residues: 476 helix: 1.71 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.17 (0.60), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.004 0.002 HIS A 348 PHE 0.022 0.002 PHE A 194 TYR 0.029 0.002 TYR A 342 ARG 0.004 0.001 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 1) link_NAG-ASN : angle 2.55681 ( 3) hydrogen bonds : bond 0.03965 ( 277) hydrogen bonds : angle 4.17335 ( 822) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.26526 ( 2) covalent geometry : bond 0.00390 ( 3831) covalent geometry : angle 0.56032 ( 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 88 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 400 SER cc_start: 0.7596 (p) cc_final: 0.7173 (t) REVERT: A 465 GLU cc_start: 0.7570 (tt0) cc_final: 0.7158 (tt0) outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 0.1089 time to fit residues: 12.2280 Evaluate side-chains 76 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 379 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 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: 0.7980 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.186923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.162402 restraints weight = 4766.531| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 1.95 r_work: 0.3891 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3909 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= 0.141 Angle : 0.535 6.713 5209 Z= 0.270 Chirality : 0.038 0.148 610 Planarity : 0.004 0.047 638 Dihedral : 3.899 21.944 537 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.67 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 (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: 1.70 (0.39), residues: 476 helix: 1.78 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.18 (0.60), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 PHE 0.016 0.001 PHE A 194 TYR 0.022 0.002 TYR A 342 ARG 0.002 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 1) link_NAG-ASN : angle 2.45960 ( 3) hydrogen bonds : bond 0.03811 ( 277) hydrogen bonds : angle 4.16280 ( 822) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.07474 ( 2) covalent geometry : bond 0.00317 ( 3831) covalent geometry : angle 0.53224 ( 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 85 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8448 (tt) REVERT: A 465 GLU cc_start: 0.7580 (tt0) cc_final: 0.7274 (tt0) outliers start: 14 outliers final: 11 residues processed: 79 average time/residue: 0.1344 time to fit residues: 14.4768 Evaluate side-chains 79 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 318 LEU 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 549 LEU Chi-restraints excluded: chain B residue 2 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 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: 0.6980 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.184941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.160377 restraints weight = 4755.626| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.95 r_work: 0.3852 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3833 Z= 0.177 Angle : 0.577 7.182 5209 Z= 0.291 Chirality : 0.038 0.143 610 Planarity : 0.004 0.047 638 Dihedral : 3.959 15.936 537 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.87 % Allowed : 17.53 % 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 (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: 1.36 (0.38), residues: 476 helix: 1.58 (0.26), residues: 369 sheet: None (None), residues: 0 loop : -1.48 (0.58), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 69 HIS 0.004 0.001 HIS A 348 PHE 0.016 0.002 PHE A 120 TYR 0.024 0.002 TYR A 342 ARG 0.002 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 1) link_NAG-ASN : angle 2.37699 ( 3) hydrogen bonds : bond 0.04035 ( 277) hydrogen bonds : angle 4.31876 ( 822) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.10382 ( 2) covalent geometry : bond 0.00413 ( 3831) covalent geometry : angle 0.57445 ( 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 85 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8446 (tt) REVERT: A 321 ILE cc_start: 0.8887 (mp) cc_final: 0.8648 (mp) REVERT: A 400 SER cc_start: 0.7545 (p) cc_final: 0.7173 (t) REVERT: A 465 GLU cc_start: 0.7622 (tt0) cc_final: 0.7322 (tt0) outliers start: 15 outliers final: 9 residues processed: 80 average time/residue: 0.1667 time to fit residues: 17.7621 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 : 0.501 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.184650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.160397 restraints weight = 4697.357| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.92 r_work: 0.3868 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3833 Z= 0.142 Angle : 0.551 7.028 5209 Z= 0.276 Chirality : 0.037 0.142 610 Planarity : 0.004 0.046 638 Dihedral : 3.900 19.011 537 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.35 % Allowed : 17.78 % 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 (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: 1.67 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.45 (0.58), residues: 105 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 0.015 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 0.00074 ( 1) link_NAG-ASN : angle 2.25452 ( 3) hydrogen bonds : bond 0.03777 ( 277) hydrogen bonds : angle 4.23645 ( 822) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.12738 ( 2) covalent geometry : bond 0.00326 ( 3831) covalent geometry : angle 0.54885 ( 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 85 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8419 (tt) REVERT: A 320 LYS cc_start: 0.8174 (mmmt) cc_final: 0.7667 (mttm) REVERT: A 321 ILE cc_start: 0.8870 (mp) cc_final: 0.8666 (mp) REVERT: A 400 SER cc_start: 0.7588 (p) cc_final: 0.7212 (t) outliers start: 13 outliers final: 10 residues processed: 81 average time/residue: 0.1221 time to fit residues: 12.9452 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 : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 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 379 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 504 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.185319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.160938 restraints weight = 4683.105| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.92 r_work: 0.3877 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3833 Z= 0.139 Angle : 0.554 6.456 5209 Z= 0.281 Chirality : 0.037 0.142 610 Planarity : 0.004 0.045 638 Dihedral : 3.910 22.065 537 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.09 % Allowed : 18.04 % 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 (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: 1.54 (0.39), residues: 476 helix: 1.74 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.55 (0.57), residues: 107 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 0.039 0.002 TYR A 335 ARG 0.002 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00093 ( 1) link_NAG-ASN : angle 2.14790 ( 3) hydrogen bonds : bond 0.03766 ( 277) hydrogen bonds : angle 4.21710 ( 822) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.08616 ( 2) covalent geometry : bond 0.00317 ( 3831) covalent geometry : angle 0.55213 ( 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 81 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8371 (tt) REVERT: A 320 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7674 (mtpp) REVERT: A 321 ILE cc_start: 0.8868 (mt) cc_final: 0.8625 (mp) REVERT: A 400 SER cc_start: 0.7595 (p) cc_final: 0.7218 (t) outliers start: 12 outliers final: 10 residues processed: 78 average time/residue: 0.1175 time to fit residues: 12.0841 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 : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 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 379 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 504 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 18 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.185788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.161590 restraints weight = 4624.948| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 1.93 r_work: 0.3888 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3833 Z= 0.137 Angle : 0.547 6.250 5209 Z= 0.276 Chirality : 0.037 0.143 610 Planarity : 0.004 0.046 638 Dihedral : 3.861 19.295 537 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.84 % Allowed : 18.04 % 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 (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: 1.62 (0.39), residues: 476 helix: 1.80 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.55 (0.56), residues: 107 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 0.021 0.002 TYR A 335 ARG 0.002 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 1) link_NAG-ASN : angle 2.07087 ( 3) hydrogen bonds : bond 0.03696 ( 277) hydrogen bonds : angle 4.19037 ( 822) SS BOND : bond 0.00017 ( 1) SS BOND : angle 0.11836 ( 2) covalent geometry : bond 0.00315 ( 3831) covalent geometry : angle 0.54476 ( 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 82 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8440 (tt) REVERT: A 320 LYS cc_start: 0.8152 (mmmt) cc_final: 0.7649 (mtpp) REVERT: A 321 ILE cc_start: 0.8850 (mt) cc_final: 0.8635 (mp) REVERT: A 400 SER cc_start: 0.7567 (p) cc_final: 0.7211 (t) REVERT: A 465 GLU cc_start: 0.7603 (tp30) cc_final: 0.7396 (tt0) outliers start: 11 outliers final: 10 residues processed: 79 average time/residue: 0.1183 time to fit residues: 12.3159 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 : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 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 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 30 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN 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 = 0.185575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.160999 restraints weight = 4677.846| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.95 r_work: 0.3880 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3833 Z= 0.146 Angle : 0.553 6.578 5209 Z= 0.281 Chirality : 0.038 0.142 610 Planarity : 0.004 0.045 638 Dihedral : 3.895 18.061 537 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.35 % Allowed : 18.04 % 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 (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: 1.61 (0.38), residues: 476 helix: 1.79 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.59 (0.57), residues: 106 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 0.019 0.001 PHE A 194 TYR 0.021 0.002 TYR A 335 ARG 0.002 0.000 ARG A 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 1) link_NAG-ASN : angle 2.01479 ( 3) hydrogen bonds : bond 0.03782 ( 277) hydrogen bonds : angle 4.21514 ( 822) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.15542 ( 2) covalent geometry : bond 0.00339 ( 3831) covalent geometry : angle 0.55143 ( 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 82 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8446 (tt) REVERT: A 320 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7675 (mtpp) REVERT: A 321 ILE cc_start: 0.8842 (mt) cc_final: 0.8617 (mp) REVERT: A 400 SER cc_start: 0.7549 (p) cc_final: 0.7175 (t) outliers start: 13 outliers final: 12 residues processed: 79 average time/residue: 0.1197 time to fit residues: 12.5654 Evaluate side-chains 81 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 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 41 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.185771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.161357 restraints weight = 4649.210| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.92 r_work: 0.3886 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3833 Z= 0.138 Angle : 0.545 6.449 5209 Z= 0.275 Chirality : 0.037 0.142 610 Planarity : 0.004 0.046 638 Dihedral : 3.845 16.572 537 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.35 % Allowed : 18.04 % 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 (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: 1.64 (0.38), residues: 476 helix: 1.82 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.58 (0.56), residues: 107 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 0.018 0.001 PHE A 194 TYR 0.017 0.002 TYR A 335 ARG 0.002 0.000 ARG A 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 1) link_NAG-ASN : angle 1.94982 ( 3) hydrogen bonds : bond 0.03752 ( 277) hydrogen bonds : angle 4.19861 ( 822) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.18597 ( 2) covalent geometry : bond 0.00317 ( 3831) covalent geometry : angle 0.54311 ( 5204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2334.88 seconds wall clock time: 41 minutes 21.66 seconds (2481.66 seconds total)