Starting phenix.real_space_refine on Wed Jul 1 21:37:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e3c_30979/07_2026/7e3c_30979.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e3c_30979/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7e3c_30979/07_2026/7e3c_30979.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e3c_30979/07_2026/7e3c_30979.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e3c_30979/07_2026/7e3c_30979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e3c_30979/07_2026/7e3c_30979.map" model { file = "/net/cci-nas-00/data/ceres_data/7e3c_30979/07_2026/7e3c_30979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e3c_30979/07_2026/7e3c_30979.cif" } 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-6108/lib/python3.11/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 chiralities: 1 Time building chain proxies: 0.93, per 1000 atoms: 0.32 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: 0.29 Conformation dependent library (CDL) restraints added in 108.5 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: 0.06 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: 0.25 Time building geometry restraints manager: 0.36 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: 1540 17.30 - 34.61: 154 34.61 - 51.91: 21 51.91 - 69.21: 5 69.21 - 86.51: 2 Dihedral angle restraints: 1722 sinusoidal: 560 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 1719 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.440 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:0.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 13.841 86.511 975 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/Z covalent geometry : bond 0.02556 / 1.80 ( 3008) covalent geometry : angle 1.55210 / 1.07 ( 4111) SS BOND : bond 0.01024 / 0.49 ( 5) SS BOND : angle 2.51963 / 1.31 ( 10) hydrogen bonds : bond 0.14312 / 9.77 ( 86) hydrogen bonds : angle 7.26782 / 4.86 ( 222) link_NAG-ASN : bond 0.00273 / 0.14 ( 1) link_NAG-ASN : angle 1.78108 / 0.90 ( 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 : 0.140 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: 0.0765 time to fit residues: 4.1492 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 : 0.116 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.061121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.051395 restraints weight = 12259.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.053209 restraints weight = 7358.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.054545 restraints weight = 4989.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055460 restraints weight = 3699.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.056223 restraints weight = 2912.724| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3014 Z= 0.162 Angle : 0.724 10.181 4124 Z= 0.378 Chirality : 0.048 0.174 452 Planarity : 0.005 0.056 540 Dihedral : 5.934 23.881 442 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % 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: -3.39 (0.38), residues: 397 helix: -3.42 (0.69), residues: 34 sheet: -1.30 (0.48), residues: 115 loop : -2.68 (0.35), residues: 248 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 0.009 0.001 PHE A 342 TRP 0.015 0.002 TRP B 36 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 3008) covalent geometry : angle 0.71876 / 0.38 ( 4111) SS BOND : bond 0.00900 / 0.43 ( 5) SS BOND : angle 1.96770 / 0.99 ( 10) hydrogen bonds : bond 0.04158 / 2.43 ( 86) hydrogen bonds : angle 5.84662 / 3.89 ( 222) link_NAG-ASN : bond 0.00309 / 0.16 ( 1) link_NAG-ASN : angle 0.82616 / 0.40 ( 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 55 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.073 Fit side-chains REVERT: A 405 ASP cc_start: 0.8617 (m-30) cc_final: 0.8309 (m-30) REVERT: A 406 GLU cc_start: 0.8726 (pt0) cc_final: 0.8394 (pt0) REVERT: A 474 GLN cc_start: 0.6753 (tp-100) cc_final: 0.6448 (tp-100) REVERT: C 31 ASN cc_start: 0.9054 (m-40) cc_final: 0.8831 (m-40) REVERT: C 48 ILE cc_start: 0.8009 (mm) cc_final: 0.7740 (tp) REVERT: C 49 TYR cc_start: 0.6323 (m-10) cc_final: 0.5854 (m-10) REVERT: B 27 LEU cc_start: 0.6237 (tp) cc_final: 0.5994 (tp) REVERT: B 45 LEU cc_start: 0.8672 (mt) cc_final: 0.8201 (mt) REVERT: B 46 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7932 (mm-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0571 time to fit residues: 3.7386 Evaluate side-chains 47 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.066 ------------------------------------------------------------------------------- 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: 0.6980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.061507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.051242 restraints weight = 12110.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.053102 restraints weight = 7145.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.054510 restraints weight = 4820.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.055563 restraints weight = 3539.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.056370 restraints weight = 2753.434| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3014 Z= 0.170 Angle : 0.712 9.842 4124 Z= 0.375 Chirality : 0.047 0.161 452 Planarity : 0.006 0.084 540 Dihedral : 5.808 28.049 442 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % 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: -3.30 (0.39), residues: 397 helix: -3.36 (0.70), residues: 34 sheet: -1.32 (0.49), residues: 116 loop : -2.58 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 346 TYR 0.018 0.001 TYR A 489 PHE 0.010 0.001 PHE A 377 TRP 0.023 0.003 TRP B 107 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 3008) covalent geometry : angle 0.70708 / 0.37 ( 4111) SS BOND : bond 0.00868 / 0.42 ( 5) SS BOND : angle 1.91270 / 0.96 ( 10) hydrogen bonds : bond 0.04163 / 2.50 ( 86) hydrogen bonds : angle 5.80312 / 3.81 ( 222) link_NAG-ASN : bond 0.00181 / 0.10 ( 1) link_NAG-ASN : angle 0.65021 / 0.31 ( 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 56 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8598 (m-30) cc_final: 0.8238 (m-30) REVERT: A 406 GLU cc_start: 0.8761 (pt0) cc_final: 0.8410 (pt0) REVERT: A 474 GLN cc_start: 0.6891 (tp-100) cc_final: 0.6520 (tp-100) REVERT: B 27 LEU cc_start: 0.6208 (tp) cc_final: 0.5729 (tp) REVERT: B 45 LEU cc_start: 0.8671 (mt) cc_final: 0.8226 (mt) REVERT: B 46 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7940 (mm-30) REVERT: B 98 ASP cc_start: 0.7567 (m-30) cc_final: 0.7360 (m-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0750 time to fit residues: 4.9506 Evaluate side-chains 46 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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: 3.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.061270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.051335 restraints weight = 12124.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.053147 restraints weight = 7239.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.054327 restraints weight = 4912.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.055400 restraints weight = 3698.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.056161 restraints weight = 2894.198| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3014 Z= 0.184 Angle : 0.717 10.078 4124 Z= 0.373 Chirality : 0.046 0.159 452 Planarity : 0.005 0.071 540 Dihedral : 5.746 23.848 442 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % 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: -3.10 (0.39), residues: 397 helix: -3.34 (0.72), residues: 34 sheet: -1.11 (0.49), residues: 114 loop : -2.45 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 457 TYR 0.014 0.001 TYR B 33 PHE 0.007 0.001 PHE A 347 TRP 0.025 0.002 TRP B 107 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 3008) covalent geometry : angle 0.71157 / 0.37 ( 4111) SS BOND : bond 0.00869 / 0.42 ( 5) SS BOND : angle 1.92478 / 0.96 ( 10) hydrogen bonds : bond 0.03848 / 2.23 ( 86) hydrogen bonds : angle 5.62418 / 3.72 ( 222) link_NAG-ASN : bond 0.00317 / 0.17 ( 1) link_NAG-ASN : angle 0.91613 / 0.47 ( 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 53 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8688 (m-30) cc_final: 0.8285 (m-30) REVERT: A 474 GLN cc_start: 0.6836 (tp-100) cc_final: 0.6544 (tp-100) REVERT: B 27 LEU cc_start: 0.6102 (tp) cc_final: 0.5693 (tp) REVERT: B 45 LEU cc_start: 0.8616 (mt) cc_final: 0.8116 (mt) REVERT: B 46 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7885 (mm-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0726 time to fit residues: 4.5303 Evaluate side-chains 47 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.111 ------------------------------------------------------------------------------- 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: 10.0000 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.059817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.049912 restraints weight = 11887.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.051575 restraints weight = 6998.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.053033 restraints weight = 4865.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.054041 restraints weight = 3530.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.054825 restraints weight = 2739.726| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1940 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= 0.220 Angle : 0.752 10.928 4124 Z= 0.392 Chirality : 0.048 0.179 452 Planarity : 0.005 0.058 540 Dihedral : 5.854 26.635 442 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % 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: -3.16 (0.40), residues: 397 helix: -3.14 (0.80), residues: 34 sheet: -1.48 (0.47), residues: 120 loop : -2.35 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 346 TYR 0.016 0.001 TYR A 453 PHE 0.008 0.001 PHE A 377 TRP 0.032 0.003 TRP B 36 HIS 0.003 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 ( 3008) covalent geometry : angle 0.74476 / 0.39 ( 4111) SS BOND : bond 0.00925 / 0.45 ( 5) SS BOND : angle 2.21526 / 1.14 ( 10) hydrogen bonds : bond 0.04055 / 2.30 ( 86) hydrogen bonds : angle 5.82664 / 3.82 ( 222) link_NAG-ASN : bond 0.00262 / 0.14 ( 1) link_NAG-ASN : angle 1.00764 / 0.50 ( 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 53 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.077 Fit side-chains REVERT: A 386 LYS cc_start: 0.8131 (mtmm) cc_final: 0.7617 (mtmm) REVERT: A 405 ASP cc_start: 0.8654 (m-30) cc_final: 0.8225 (m-30) REVERT: A 442 ASP cc_start: 0.7985 (m-30) cc_final: 0.7771 (m-30) REVERT: A 474 GLN cc_start: 0.6622 (tp-100) cc_final: 0.6401 (tp-100) REVERT: B 27 LEU cc_start: 0.6420 (tp) cc_final: 0.5960 (tp) REVERT: B 45 LEU cc_start: 0.8777 (mt) cc_final: 0.8231 (mt) REVERT: B 46 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7907 (mm-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0754 time to fit residues: 4.7573 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 : 0.135 ------------------------------------------------------------------------------- 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: 0.9980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 0.0870 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.060947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.050959 restraints weight = 11701.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.052783 restraints weight = 6919.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.054138 restraints weight = 4680.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055173 restraints weight = 3460.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.055915 restraints weight = 2674.118| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3014 Z= 0.151 Angle : 0.711 9.942 4124 Z= 0.368 Chirality : 0.046 0.152 452 Planarity : 0.005 0.060 540 Dihedral : 5.611 23.810 442 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -3.05 (0.40), residues: 397 helix: -3.26 (0.72), residues: 34 sheet: -1.43 (0.46), residues: 120 loop : -2.23 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 346 TYR 0.013 0.001 TYR B 33 PHE 0.011 0.001 PHE A 347 TRP 0.024 0.002 TRP B 36 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 3008) covalent geometry : angle 0.70404 / 0.37 ( 4111) SS BOND : bond 0.00817 / 0.39 ( 5) SS BOND : angle 2.12252 / 1.08 ( 10) hydrogen bonds : bond 0.03732 / 2.10 ( 86) hydrogen bonds : angle 5.77674 / 3.83 ( 222) link_NAG-ASN : bond 0.00113 / 0.06 ( 1) link_NAG-ASN : angle 0.65103 / 0.31 ( 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 53 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7562 (mtmm) REVERT: A 405 ASP cc_start: 0.8684 (m-30) cc_final: 0.8310 (m-30) REVERT: A 406 GLU cc_start: 0.9059 (pt0) cc_final: 0.8808 (pt0) REVERT: B 27 LEU cc_start: 0.6448 (tp) cc_final: 0.5929 (tp) REVERT: B 45 LEU cc_start: 0.8669 (mt) cc_final: 0.8143 (mt) REVERT: B 46 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 98 ASP cc_start: 0.7817 (m-30) cc_final: 0.7544 (m-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0666 time to fit residues: 4.2637 Evaluate side-chains 46 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.060518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.050565 restraints weight = 11873.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.052227 restraints weight = 6930.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.053710 restraints weight = 4804.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.054722 restraints weight = 3491.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055538 restraints weight = 2704.783| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3014 Z= 0.191 Angle : 0.736 9.288 4124 Z= 0.380 Chirality : 0.047 0.156 452 Planarity : 0.005 0.053 540 Dihedral : 5.727 23.155 442 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % 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: -3.06 (0.40), residues: 397 helix: -3.20 (0.74), residues: 34 sheet: -1.43 (0.46), residues: 120 loop : -2.25 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 346 TYR 0.014 0.002 TYR B 33 PHE 0.007 0.001 PHE A 347 TRP 0.012 0.002 TRP B 107 HIS 0.002 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 3008) covalent geometry : angle 0.72853 / 0.38 ( 4111) SS BOND : bond 0.00899 / 0.43 ( 5) SS BOND : angle 2.23230 / 1.10 ( 10) hydrogen bonds : bond 0.03745 / 2.12 ( 86) hydrogen bonds : angle 5.71529 / 3.78 ( 222) link_NAG-ASN : bond 0.00215 / 0.11 ( 1) link_NAG-ASN : angle 0.83660 / 0.41 ( 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 : 0.066 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8700 (m-30) cc_final: 0.8265 (m-30) REVERT: B 27 LEU cc_start: 0.6717 (tp) cc_final: 0.6184 (tp) REVERT: B 45 LEU cc_start: 0.8686 (mt) cc_final: 0.8195 (mt) REVERT: B 46 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7906 (mm-30) REVERT: B 98 ASP cc_start: 0.7799 (m-30) cc_final: 0.7033 (m-30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0431 time to fit residues: 2.6700 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 : 0.065 ------------------------------------------------------------------------------- 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: 0.8980 chunk 35 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.0270 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.062169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.052093 restraints weight = 11894.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.053938 restraints weight = 7047.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.055016 restraints weight = 4761.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.056268 restraints weight = 3647.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.056944 restraints weight = 2807.294| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3014 Z= 0.150 Angle : 0.709 8.534 4124 Z= 0.367 Chirality : 0.046 0.151 452 Planarity : 0.005 0.054 540 Dihedral : 5.570 25.038 442 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -2.93 (0.40), residues: 397 helix: -3.22 (0.72), residues: 34 sheet: -1.28 (0.47), residues: 118 loop : -2.17 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 346 TYR 0.013 0.001 TYR A 453 PHE 0.011 0.001 PHE A 377 TRP 0.057 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 3008) covalent geometry : angle 0.70098 / 0.36 ( 4111) SS BOND : bond 0.00858 / 0.41 ( 5) SS BOND : angle 2.31147 / 1.18 ( 10) hydrogen bonds : bond 0.03723 / 2.06 ( 86) hydrogen bonds : angle 5.75385 / 3.81 ( 222) link_NAG-ASN : bond 0.00243 / 0.13 ( 1) link_NAG-ASN : angle 0.72816 / 0.36 ( 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 52 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8632 (m-30) cc_final: 0.8250 (m-30) REVERT: A 406 GLU cc_start: 0.9040 (pt0) cc_final: 0.8752 (pt0) REVERT: A 474 GLN cc_start: 0.6905 (tp-100) cc_final: 0.6520 (tp-100) REVERT: B 45 LEU cc_start: 0.8642 (mt) cc_final: 0.8090 (mt) REVERT: B 46 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7957 (mm-30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0507 time to fit residues: 3.1502 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 : 0.108 ------------------------------------------------------------------------------- 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: 0.6980 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 0.0020 chunk 34 optimal weight: 0.0970 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.061716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.051587 restraints weight = 11934.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.053296 restraints weight = 6999.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.054764 restraints weight = 4850.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.055813 restraints weight = 3525.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.056557 restraints weight = 2736.353| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2556 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= 0.144 Angle : 0.703 8.757 4124 Z= 0.362 Chirality : 0.046 0.146 452 Planarity : 0.004 0.051 540 Dihedral : 5.531 24.090 442 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.38 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: -2.90 (0.40), residues: 397 helix: -3.30 (0.70), residues: 34 sheet: -1.23 (0.47), residues: 113 loop : -2.14 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 454 TYR 0.016 0.001 TYR A 453 PHE 0.008 0.001 PHE A 347 TRP 0.045 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 3008) covalent geometry : angle 0.69539 / 0.36 ( 4111) SS BOND : bond 0.00803 / 0.38 ( 5) SS BOND : angle 2.14564 / 1.08 ( 10) hydrogen bonds : bond 0.03582 / 1.94 ( 86) hydrogen bonds : angle 5.56049 / 3.74 ( 222) link_NAG-ASN : bond 0.00199 / 0.10 ( 1) link_NAG-ASN : angle 0.67451 / 0.34 ( 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 : 0.067 Fit side-chains REVERT: A 405 ASP cc_start: 0.8676 (m-30) cc_final: 0.8278 (m-30) REVERT: A 406 GLU cc_start: 0.8965 (pt0) cc_final: 0.8765 (pt0) REVERT: A 474 GLN cc_start: 0.6874 (tp-100) cc_final: 0.6568 (tp-100) REVERT: B 45 LEU cc_start: 0.8643 (mt) cc_final: 0.8124 (mt) REVERT: B 46 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7981 (mm-30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0370 time to fit residues: 2.3811 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: 1.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.0470 chunk 6 optimal weight: 0.3980 chunk 26 optimal weight: 0.0040 overall best weight: 0.3090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.062968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.052779 restraints weight = 11878.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.054647 restraints weight = 6985.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.055990 restraints weight = 4719.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.057005 restraints weight = 3483.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.057801 restraints weight = 2726.821| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2813 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= 0.120 Angle : 0.689 9.135 4124 Z= 0.354 Chirality : 0.045 0.149 452 Planarity : 0.004 0.050 540 Dihedral : 5.458 25.467 442 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -2.80 (0.40), residues: 397 helix: -3.30 (0.69), residues: 34 sheet: -1.18 (0.48), residues: 113 loop : -2.05 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.012 0.001 TYR B 101 PHE 0.009 0.001 PHE A 377 TRP 0.015 0.002 TRP B 107 HIS 0.001 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 3008) covalent geometry : angle 0.68356 / 0.35 ( 4111) SS BOND : bond 0.00731 / 0.35 ( 5) SS BOND : angle 1.90009 / 0.94 ( 10) hydrogen bonds : bond 0.03418 / 1.90 ( 86) hydrogen bonds : angle 5.34984 / 3.58 ( 222) link_NAG-ASN : bond 0.00189 / 0.10 ( 1) link_NAG-ASN : angle 0.42442 / 0.21 ( 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 55 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8624 (m-30) cc_final: 0.8292 (m-30) REVERT: A 406 GLU cc_start: 0.9010 (pt0) cc_final: 0.8730 (pt0) REVERT: A 474 GLN cc_start: 0.6900 (tp-100) cc_final: 0.6529 (tp-100) REVERT: B 45 LEU cc_start: 0.8606 (mt) cc_final: 0.8021 (mt) REVERT: B 105 ASP cc_start: 0.8027 (t0) cc_final: 0.7795 (t0) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0546 time to fit residues: 3.7387 Evaluate side-chains 44 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.067 ------------------------------------------------------------------------------- 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: 1.9990 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.061358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.051065 restraints weight = 11861.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.052948 restraints weight = 6954.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.054348 restraints weight = 4683.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.055269 restraints weight = 3447.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.056086 restraints weight = 2720.710| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2625 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= 0.179 Angle : 0.728 9.624 4124 Z= 0.373 Chirality : 0.047 0.149 452 Planarity : 0.004 0.052 540 Dihedral : 5.562 23.911 442 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -2.84 (0.40), residues: 397 helix: -2.98 (0.68), residues: 40 sheet: -1.17 (0.48), residues: 112 loop : -2.12 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.014 0.001 TYR A 453 PHE 0.008 0.001 PHE A 377 TRP 0.062 0.004 TRP B 36 HIS 0.003 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 3008) covalent geometry : angle 0.72041 / 0.37 ( 4111) SS BOND : bond 0.00860 / 0.42 ( 5) SS BOND : angle 2.31101 / 1.19 ( 10) hydrogen bonds : bond 0.03899 / 2.10 ( 86) hydrogen bonds : angle 5.47897 / 3.67 ( 222) link_NAG-ASN : bond 0.00167 / 0.09 ( 1) link_NAG-ASN : angle 0.60294 / 0.30 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 633.65 seconds wall clock time: 11 minutes 38.17 seconds (698.17 seconds total)