Starting phenix.real_space_refine on Tue Mar 3 11:16:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e3c_30979/03_2026/7e3c_30979.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e3c_30979/03_2026/7e3c_30979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e3c_30979/03_2026/7e3c_30979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e3c_30979/03_2026/7e3c_30979.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e3c_30979/03_2026/7e3c_30979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e3c_30979/03_2026/7e3c_30979.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 15 5.16 5 C 1865 2.51 5 N 493 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2937 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "C" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 655 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 3, 'ASP:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 732 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 2, 'TRANS': 106} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 4, 'ASP:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 46 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: 0.91, per 1000 atoms: 0.31 Number of scatterers: 2937 At special positions: 0 Unit cell: (64.133, 56.524, 95.656, 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 15 16.00 O 564 8.00 N 493 7.00 C 1865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " 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 343 " Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 119.3 milliseconds 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 9.9% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.962A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.880A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.456A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'C' and resid 57 through 61 removed outlier: 4.282A pdb=" N ARG C 61 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.206A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 13 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.173A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 removed outlier: 3.613A pdb=" N TYR B 79 " --> pdb=" O ILE B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 57 through 59 removed outlier: 4.167A pdb=" N TYR B 33 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B 96 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG B 97 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 59 92 hydrogen bonds defined for protein. 222 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: 0.42 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.52: 2204 1.52 - 1.81: 801 1.81 - 2.11: 2 2.11 - 2.40: 0 2.40 - 2.69: 1 Bond restraints: 3008 Sorted by residual: bond pdb=" C HIS B 72 " pdb=" N ASN B 76 " ideal model delta sigma weight residual 1.332 2.695 -1.362 1.40e-02 5.10e+03 9.47e+03 bond pdb=" CA ILE B 69 " pdb=" CB ILE B 69 " ideal model delta sigma weight residual 1.551 1.530 0.020 1.08e-02 8.57e+03 3.50e+00 bond pdb=" N ARG B 71 " pdb=" CA ARG B 71 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.49e+00 bond pdb=" N HIS B 72 " pdb=" CA HIS B 72 " ideal model delta sigma weight residual 1.461 1.483 -0.022 1.20e-02 6.94e+03 3.22e+00 bond pdb=" C PRO C 95 " pdb=" N PRO C 96 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.74e+00 ... (remaining 3003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.57: 4107 10.57 - 21.14: 1 21.14 - 31.71: 0 31.71 - 42.28: 1 42.28 - 52.85: 2 Bond angle restraints: 4111 Sorted by residual: angle pdb=" O HIS B 72 " pdb=" C HIS B 72 " pdb=" N ASN B 76 " ideal model delta sigma weight residual 123.26 70.41 52.85 1.24e+00 6.50e-01 1.82e+03 angle pdb=" CA HIS B 72 " pdb=" C HIS B 72 " pdb=" N ASN B 76 " ideal model delta sigma weight residual 116.71 66.92 49.79 1.30e+00 5.92e-01 1.47e+03 angle pdb=" C HIS B 72 " pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta sigma weight residual 121.54 156.28 -34.74 1.91e+00 2.74e-01 3.31e+02 angle pdb=" N PRO C 59 " pdb=" CA PRO C 59 " pdb=" CB PRO C 59 " ideal model delta sigma weight residual 103.20 110.16 -6.96 9.50e-01 1.11e+00 5.37e+01 angle pdb=" N PRO B 14 " pdb=" CA PRO B 14 " pdb=" CB PRO B 14 " ideal model delta sigma weight residual 103.25 110.58 -7.33 1.05e+00 9.07e-01 4.87e+01 ... (remaining 4106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 1559 17.30 - 34.61: 154 34.61 - 51.91: 21 51.91 - 69.21: 7 69.21 - 86.51: 2 Dihedral angle restraints: 1743 sinusoidal: 581 harmonic: 1162 Sorted by residual: dihedral pdb=" CA HIS B 72 " pdb=" C HIS B 72 " pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta harmonic sigma weight residual -180.00 -117.44 -62.56 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 37.09 55.91 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 148.00 -55.00 1 1.00e+01 1.00e-02 4.09e+01 ... (remaining 1740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 331 0.052 - 0.104: 97 0.104 - 0.156: 18 0.156 - 0.208: 3 0.208 - 0.260: 3 Chirality restraints: 452 Sorted by residual: chirality pdb=" CA PRO C 59 " pdb=" N PRO C 59 " pdb=" C PRO C 59 " pdb=" CB PRO C 59 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PRO C 8 " pdb=" N PRO C 8 " pdb=" C PRO C 8 " pdb=" CB PRO C 8 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 449 not shown) Planarity restraints: 541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 72 " 0.184 2.00e-02 2.50e+03 2.33e-01 5.43e+02 pdb=" C HIS B 72 " -0.351 2.00e-02 2.50e+03 pdb=" O HIS B 72 " 0.235 2.00e-02 2.50e+03 pdb=" N ASN B 76 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 94 " 0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO C 95 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 36 " -0.019 2.00e-02 2.50e+03 1.44e-02 5.15e+00 pdb=" CG TRP B 36 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 36 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 36 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 36 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 36 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 36 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 36 " -0.002 2.00e-02 2.50e+03 ... (remaining 538 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 136 2.70 - 3.25: 3043 3.25 - 3.80: 4610 3.80 - 4.35: 5626 4.35 - 4.90: 9487 Nonbonded interactions: 22902 Sorted by model distance: nonbonded pdb=" NH1 ARG A 457 " pdb=" O SER A 459 " model vdw 2.151 3.120 nonbonded pdb=" O LEU B 99 " pdb=" N TYR B 102 " model vdw 2.203 3.120 nonbonded pdb=" NZ LYS A 417 " pdb=" OD2 ASP B 100 " model vdw 2.233 3.120 nonbonded pdb=" O LEU A 455 " pdb=" OH TYR B 33 " model vdw 2.253 3.040 nonbonded pdb=" O ASP C 17 " pdb=" N LEU C 78 " model vdw 2.272 3.120 ... (remaining 22897 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 group one per residue 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 5.420 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 : 0.026 1.362 3014 Z= 1.795 Angle : 1.555 52.846 4124 Z= 1.075 Chirality : 0.053 0.260 452 Planarity : 0.012 0.233 540 Dihedral : 13.929 86.511 996 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.51 % Allowed : 17.22 % Favored : 82.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.39), residues: 395 helix: -3.32 (0.69), residues: 34 sheet: -1.46 (0.48), residues: 119 loop : -2.92 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 97 TYR 0.022 0.002 TYR A 453 PHE 0.015 0.002 PHE A 342 TRP 0.038 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.02556 ( 3008) covalent geometry : angle 1.55210 ( 4111) SS BOND : bond 0.01024 ( 5) SS BOND : angle 2.51963 ( 10) hydrogen bonds : bond 0.14312 ( 86) hydrogen bonds : angle 7.26782 ( 222) link_NAG-ASN : bond 0.00273 ( 1) link_NAG-ASN : angle 1.78108 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8126 (mtmm) cc_final: 0.7756 (mtmm) REVERT: A 405 ASP cc_start: 0.8591 (m-30) cc_final: 0.8280 (m-30) REVERT: A 406 GLU cc_start: 0.8704 (pt0) cc_final: 0.8418 (pt0) REVERT: A 474 GLN cc_start: 0.6423 (tp-100) cc_final: 0.6206 (tp-100) REVERT: B 45 LEU cc_start: 0.8621 (mt) cc_final: 0.8136 (mt) REVERT: B 104 MET cc_start: 0.7456 (mtp) cc_final: 0.7086 (mtm) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0793 time to fit residues: 4.2801 Evaluate side-chains 41 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.0000 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 = 0.3072 r_free = 0.3072 target = 0.060997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.051323 restraints weight = 12267.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.053110 restraints weight = 7329.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.054458 restraints weight = 4968.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.055408 restraints weight = 3696.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.056007 restraints weight = 2882.735| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3014 Z= 0.164 Angle : 0.727 10.317 4124 Z= 0.379 Chirality : 0.048 0.171 452 Planarity : 0.005 0.056 540 Dihedral : 6.639 46.943 463 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.85 % Favored : 86.15 % Rotamer: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.39), residues: 397 helix: -3.38 (0.71), residues: 34 sheet: -1.42 (0.48), residues: 117 loop : -2.70 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 457 TYR 0.016 0.001 TYR B 33 PHE 0.008 0.001 PHE A 342 TRP 0.013 0.002 TRP B 36 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3008) covalent geometry : angle 0.72161 ( 4111) SS BOND : bond 0.00905 ( 5) SS BOND : angle 1.98600 ( 10) hydrogen bonds : bond 0.04232 ( 86) hydrogen bonds : angle 5.87443 ( 222) link_NAG-ASN : bond 0.00285 ( 1) link_NAG-ASN : angle 0.91262 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.089 Fit side-chains REVERT: A 405 ASP cc_start: 0.8631 (m-30) cc_final: 0.8311 (m-30) REVERT: A 406 GLU cc_start: 0.8743 (pt0) cc_final: 0.8412 (pt0) REVERT: A 474 GLN cc_start: 0.6816 (tp-100) cc_final: 0.6489 (tp-100) REVERT: C 49 TYR cc_start: 0.6317 (m-10) cc_final: 0.5953 (m-10) REVERT: B 27 LEU cc_start: 0.6244 (tp) cc_final: 0.5992 (tp) REVERT: B 45 LEU cc_start: 0.8711 (mt) cc_final: 0.8230 (mt) REVERT: B 46 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7952 (mm-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0647 time to fit residues: 4.1444 Evaluate side-chains 45 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3053 r_free = 0.3053 target = 0.060830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.050525 restraints weight = 12160.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.052388 restraints weight = 7207.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.053787 restraints weight = 4874.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.054837 restraints weight = 3571.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.055647 restraints weight = 2777.520| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3014 Z= 0.200 Angle : 0.736 10.389 4124 Z= 0.386 Chirality : 0.048 0.164 452 Planarity : 0.006 0.084 540 Dihedral : 6.298 34.789 463 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.39), residues: 397 helix: -3.32 (0.72), residues: 34 sheet: -1.40 (0.48), residues: 116 loop : -2.65 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 457 TYR 0.021 0.002 TYR A 489 PHE 0.010 0.001 PHE A 377 TRP 0.025 0.003 TRP B 107 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 3008) covalent geometry : angle 0.72973 ( 4111) SS BOND : bond 0.00915 ( 5) SS BOND : angle 2.04565 ( 10) hydrogen bonds : bond 0.04301 ( 86) hydrogen bonds : angle 5.79690 ( 222) link_NAG-ASN : bond 0.00193 ( 1) link_NAG-ASN : angle 0.89134 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8600 (m-30) cc_final: 0.8246 (m-30) REVERT: A 406 GLU cc_start: 0.8756 (pt0) cc_final: 0.8388 (pt0) REVERT: A 474 GLN cc_start: 0.6859 (tp-100) cc_final: 0.6518 (tp-100) REVERT: B 27 LEU cc_start: 0.6261 (tp) cc_final: 0.5772 (tp) REVERT: B 45 LEU cc_start: 0.8708 (mt) cc_final: 0.8216 (mt) REVERT: B 46 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7919 (mm-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0711 time to fit residues: 4.5841 Evaluate side-chains 45 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.0370 chunk 25 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3089 r_free = 0.3089 target = 0.061986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.052056 restraints weight = 12086.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.053650 restraints weight = 7186.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.055039 restraints weight = 5050.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.055924 restraints weight = 3715.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056808 restraints weight = 2936.051| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3014 Z= 0.144 Angle : 0.692 9.273 4124 Z= 0.359 Chirality : 0.046 0.142 452 Planarity : 0.005 0.069 540 Dihedral : 5.686 22.952 463 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.39), residues: 397 helix: -3.36 (0.70), residues: 34 sheet: -1.12 (0.49), residues: 115 loop : -2.46 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 457 TYR 0.014 0.001 TYR C 94 PHE 0.009 0.001 PHE A 347 TRP 0.023 0.002 TRP B 107 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3008) covalent geometry : angle 0.68714 ( 4111) SS BOND : bond 0.00817 ( 5) SS BOND : angle 1.80331 ( 10) hydrogen bonds : bond 0.03684 ( 86) hydrogen bonds : angle 5.70203 ( 222) link_NAG-ASN : bond 0.00100 ( 1) link_NAG-ASN : angle 0.60837 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.119 Fit side-chains REVERT: A 405 ASP cc_start: 0.8662 (m-30) cc_final: 0.8283 (m-30) REVERT: A 474 GLN cc_start: 0.6839 (tp-100) cc_final: 0.6504 (tp-100) REVERT: C 31 ASN cc_start: 0.9065 (m-40) cc_final: 0.8845 (m-40) REVERT: B 27 LEU cc_start: 0.6162 (tp) cc_final: 0.5732 (tp) REVERT: B 45 LEU cc_start: 0.8587 (mt) cc_final: 0.8126 (mt) REVERT: B 98 ASP cc_start: 0.7725 (m-30) cc_final: 0.7493 (m-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0883 time to fit residues: 5.6661 Evaluate side-chains 43 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 13 optimal weight: 0.0000 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.3080 r_free = 0.3080 target = 0.061217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.051271 restraints weight = 11765.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.053084 restraints weight = 6951.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.054476 restraints weight = 4710.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.055454 restraints weight = 3459.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.056239 restraints weight = 2697.842| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3014 Z= 0.161 Angle : 0.710 9.438 4124 Z= 0.369 Chirality : 0.047 0.175 452 Planarity : 0.005 0.056 540 Dihedral : 5.594 24.626 463 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.40), residues: 397 helix: -3.23 (0.74), residues: 34 sheet: -1.26 (0.48), residues: 117 loop : -2.38 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 457 TYR 0.012 0.001 TYR B 101 PHE 0.010 0.001 PHE A 377 TRP 0.020 0.002 TRP B 107 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3008) covalent geometry : angle 0.70442 ( 4111) SS BOND : bond 0.00839 ( 5) SS BOND : angle 1.89052 ( 10) hydrogen bonds : bond 0.03742 ( 86) hydrogen bonds : angle 5.74240 ( 222) link_NAG-ASN : bond 0.00171 ( 1) link_NAG-ASN : angle 0.56607 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8707 (m-30) cc_final: 0.8253 (m-30) REVERT: A 406 GLU cc_start: 0.8981 (pt0) cc_final: 0.8714 (pt0) REVERT: A 474 GLN cc_start: 0.6821 (tp-100) cc_final: 0.6556 (tp-100) REVERT: B 27 LEU cc_start: 0.6120 (tp) cc_final: 0.5688 (tp) REVERT: B 45 LEU cc_start: 0.8569 (mt) cc_final: 0.8095 (mt) REVERT: B 98 ASP cc_start: 0.7961 (m-30) cc_final: 0.7715 (m-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0768 time to fit residues: 5.0910 Evaluate side-chains 45 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3061 r_free = 0.3061 target = 0.060513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.050680 restraints weight = 11751.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.052482 restraints weight = 6909.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.053843 restraints weight = 4655.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.054834 restraints weight = 3433.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.055616 restraints weight = 2666.845| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3014 Z= 0.198 Angle : 0.729 10.203 4124 Z= 0.378 Chirality : 0.047 0.155 452 Planarity : 0.005 0.058 540 Dihedral : 5.671 24.576 463 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.40), residues: 397 helix: -3.11 (0.78), residues: 34 sheet: -1.32 (0.47), residues: 117 loop : -2.35 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 346 TYR 0.015 0.001 TYR B 33 PHE 0.006 0.001 PHE A 342 TRP 0.035 0.003 TRP B 36 HIS 0.002 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 3008) covalent geometry : angle 0.72358 ( 4111) SS BOND : bond 0.00900 ( 5) SS BOND : angle 2.00468 ( 10) hydrogen bonds : bond 0.03870 ( 86) hydrogen bonds : angle 5.71329 ( 222) link_NAG-ASN : bond 0.00109 ( 1) link_NAG-ASN : angle 0.57653 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8632 (m-30) cc_final: 0.8228 (m-30) REVERT: B 27 LEU cc_start: 0.6424 (tp) cc_final: 0.6009 (tp) REVERT: B 45 LEU cc_start: 0.8634 (mt) cc_final: 0.8110 (mt) REVERT: B 46 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7939 (mm-30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0751 time to fit residues: 4.6536 Evaluate side-chains 41 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3054 r_free = 0.3054 target = 0.060382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.050377 restraints weight = 11913.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.052180 restraints weight = 7032.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.053550 restraints weight = 4754.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.054437 restraints weight = 3494.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.055207 restraints weight = 2755.809| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3014 Z= 0.198 Angle : 0.748 10.438 4124 Z= 0.386 Chirality : 0.047 0.163 452 Planarity : 0.005 0.051 540 Dihedral : 5.738 25.268 463 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.40), residues: 397 helix: -3.12 (0.78), residues: 34 sheet: -1.43 (0.46), residues: 120 loop : -2.35 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 346 TYR 0.014 0.001 TYR A 453 PHE 0.007 0.001 PHE A 377 TRP 0.028 0.002 TRP B 36 HIS 0.003 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 3008) covalent geometry : angle 0.74112 ( 4111) SS BOND : bond 0.00854 ( 5) SS BOND : angle 2.18271 ( 10) hydrogen bonds : bond 0.03837 ( 86) hydrogen bonds : angle 5.80878 ( 222) link_NAG-ASN : bond 0.00173 ( 1) link_NAG-ASN : angle 0.73820 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.084 Fit side-chains REVERT: A 405 ASP cc_start: 0.8634 (m-30) cc_final: 0.8225 (m-30) REVERT: A 406 GLU cc_start: 0.9053 (pt0) cc_final: 0.8809 (pt0) REVERT: B 27 LEU cc_start: 0.6624 (tp) cc_final: 0.6121 (tp) REVERT: B 45 LEU cc_start: 0.8669 (mt) cc_final: 0.8187 (mt) REVERT: B 46 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7952 (mm-30) REVERT: B 98 ASP cc_start: 0.7820 (m-30) cc_final: 0.7257 (m-30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0688 time to fit residues: 4.2093 Evaluate side-chains 40 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 6 optimal weight: 0.0980 chunk 31 optimal weight: 0.4980 chunk 13 optimal weight: 0.0010 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.2524 ------------------------------------------------------------------------------- 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 = 0.3139 r_free = 0.3139 target = 0.063683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.053743 restraints weight = 11889.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.055556 restraints weight = 7131.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.056974 restraints weight = 4831.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.057894 restraints weight = 3541.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.058663 restraints weight = 2780.254| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3014 Z= 0.119 Angle : 0.689 8.400 4124 Z= 0.357 Chirality : 0.045 0.157 452 Planarity : 0.004 0.056 540 Dihedral : 5.465 22.400 463 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.40), residues: 397 helix: -3.37 (0.67), residues: 34 sheet: -1.26 (0.47), residues: 120 loop : -2.14 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.012 0.001 TYR A 453 PHE 0.014 0.001 PHE A 347 TRP 0.017 0.002 TRP B 36 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3008) covalent geometry : angle 0.68291 ( 4111) SS BOND : bond 0.00796 ( 5) SS BOND : angle 2.01999 ( 10) hydrogen bonds : bond 0.03366 ( 86) hydrogen bonds : angle 5.71579 ( 222) link_NAG-ASN : bond 0.00098 ( 1) link_NAG-ASN : angle 0.40907 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8680 (m-30) cc_final: 0.8322 (m-30) REVERT: A 406 GLU cc_start: 0.8744 (pt0) cc_final: 0.8522 (pt0) REVERT: A 474 GLN cc_start: 0.6896 (tp-100) cc_final: 0.6588 (tp-100) REVERT: B 45 LEU cc_start: 0.8543 (mt) cc_final: 0.8064 (mt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0649 time to fit residues: 4.5056 Evaluate side-chains 43 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3084 r_free = 0.3084 target = 0.061425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.051265 restraints weight = 11926.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.053123 restraints weight = 7049.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.054550 restraints weight = 4738.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.055451 restraints weight = 3465.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.056279 restraints weight = 2732.748| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3014 Z= 0.174 Angle : 0.714 9.192 4124 Z= 0.369 Chirality : 0.046 0.147 452 Planarity : 0.004 0.046 540 Dihedral : 5.553 25.729 463 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.40), residues: 397 helix: -3.12 (0.73), residues: 34 sheet: -1.39 (0.47), residues: 120 loop : -2.17 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 457 TYR 0.017 0.001 TYR A 453 PHE 0.011 0.001 PHE A 347 TRP 0.060 0.003 TRP B 36 HIS 0.002 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 3008) covalent geometry : angle 0.70470 ( 4111) SS BOND : bond 0.00866 ( 5) SS BOND : angle 2.45243 ( 10) hydrogen bonds : bond 0.03710 ( 86) hydrogen bonds : angle 5.64182 ( 222) link_NAG-ASN : bond 0.00116 ( 1) link_NAG-ASN : angle 0.40690 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8649 (m-30) cc_final: 0.8268 (m-30) REVERT: A 406 GLU cc_start: 0.9017 (pt0) cc_final: 0.8766 (pt0) REVERT: A 474 GLN cc_start: 0.6894 (tp-100) cc_final: 0.6571 (tp-100) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0665 time to fit residues: 4.0960 Evaluate side-chains 41 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 0.0010 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.3099 r_free = 0.3099 target = 0.061858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.051762 restraints weight = 11882.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.053636 restraints weight = 7082.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055104 restraints weight = 4771.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056082 restraints weight = 3491.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.056830 restraints weight = 2709.503| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3014 Z= 0.155 Angle : 0.706 9.338 4124 Z= 0.365 Chirality : 0.046 0.141 452 Planarity : 0.004 0.057 540 Dihedral : 5.557 23.738 463 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.40), residues: 397 helix: -3.09 (0.74), residues: 34 sheet: -1.31 (0.47), residues: 120 loop : -2.17 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 457 TYR 0.014 0.001 TYR A 453 PHE 0.010 0.001 PHE A 347 TRP 0.053 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 3008) covalent geometry : angle 0.69822 ( 4111) SS BOND : bond 0.00824 ( 5) SS BOND : angle 2.25846 ( 10) hydrogen bonds : bond 0.03665 ( 86) hydrogen bonds : angle 5.62777 ( 222) link_NAG-ASN : bond 0.00164 ( 1) link_NAG-ASN : angle 0.26648 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8654 (m-30) cc_final: 0.8258 (m-30) REVERT: A 406 GLU cc_start: 0.8859 (pt0) cc_final: 0.8658 (pt0) REVERT: A 474 GLN cc_start: 0.6850 (tp-100) cc_final: 0.6573 (tp-100) REVERT: B 46 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7976 (mm-30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0633 time to fit residues: 4.0815 Evaluate side-chains 41 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3087 r_free = 0.3087 target = 0.061710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.051745 restraints weight = 11844.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.053512 restraints weight = 7183.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.054816 restraints weight = 4915.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.055815 restraints weight = 3676.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.056443 restraints weight = 2888.818| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3014 Z= 0.166 Angle : 0.712 9.522 4124 Z= 0.370 Chirality : 0.046 0.147 452 Planarity : 0.004 0.047 540 Dihedral : 5.614 26.590 463 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.40), residues: 397 helix: -3.01 (0.76), residues: 34 sheet: -1.23 (0.47), residues: 118 loop : -2.18 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 454 TYR 0.017 0.001 TYR A 453 PHE 0.010 0.001 PHE A 347 TRP 0.050 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 3008) covalent geometry : angle 0.70471 ( 4111) SS BOND : bond 0.00846 ( 5) SS BOND : angle 2.26774 ( 10) hydrogen bonds : bond 0.03721 ( 86) hydrogen bonds : angle 5.58752 ( 222) link_NAG-ASN : bond 0.00164 ( 1) link_NAG-ASN : angle 0.32024 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 690.01 seconds wall clock time: 12 minutes 31.87 seconds (751.87 seconds total)