Starting phenix.real_space_refine on Wed Jul 23 10:19:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e3c_30979/07_2025/7e3c_30979.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e3c_30979/07_2025/7e3c_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7e3c_30979/07_2025/7e3c_30979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e3c_30979/07_2025/7e3c_30979.map" model { file = "/net/cci-nas-00/data/ceres_data/7e3c_30979/07_2025/7e3c_30979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e3c_30979/07_2025/7e3c_30979.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'ARG:plan': 3, 'GLU:plan': 1, 'ASP: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: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} 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: 3.04, per 1000 atoms: 1.04 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: 0.67 Conformation dependent library (CDL) restraints added in 358.7 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: 0.37 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: 0.75 Time building geometry restraints manager: 0.83 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: 1.350 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.740 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.038 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.015 0.002 PHE A 342 TYR 0.022 0.002 TYR A 453 ARG 0.005 0.001 ARG B 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 1) link_NAG-ASN : angle 1.78108 ( 3) hydrogen bonds : bond 0.14312 ( 86) hydrogen bonds : angle 7.26782 ( 222) SS BOND : bond 0.01024 ( 5) SS BOND : angle 2.51963 ( 10) covalent geometry : bond 0.02556 ( 3008) covalent geometry : angle 1.55210 ( 4111) *********************** 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 : 0.323 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: 0.8420 (pt0) REVERT: A 474 GLN cc_start: 0.6423 (tp-100) cc_final: 0.6205 (tp-100) REVERT: B 45 LEU cc_start: 0.8621 (mt) cc_final: 0.8137 (mt) REVERT: B 104 MET cc_start: 0.7456 (mtp) cc_final: 0.7089 (mtm) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1752 time to fit residues: 9.4758 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 : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.0370 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 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 = 0.3081 r_free = 0.3081 target = 0.061324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.051691 restraints weight = 12181.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.053486 restraints weight = 7312.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.054810 restraints weight = 4959.268| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3014 Z= 0.151 Angle : 0.716 9.909 4124 Z= 0.374 Chirality : 0.047 0.167 452 Planarity : 0.005 0.056 540 Dihedral : 6.514 44.711 463 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.85 % Favored : 87.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.39), residues: 397 helix: -3.39 (0.70), residues: 34 sheet: -1.26 (0.49), residues: 115 loop : -2.67 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 36 HIS 0.001 0.001 HIS A 519 PHE 0.008 0.001 PHE A 342 TYR 0.016 0.001 TYR B 33 ARG 0.004 0.000 ARG A 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 1) link_NAG-ASN : angle 0.84504 ( 3) hydrogen bonds : bond 0.04080 ( 86) hydrogen bonds : angle 5.81748 ( 222) SS BOND : bond 0.00883 ( 5) SS BOND : angle 1.93453 ( 10) covalent geometry : bond 0.00347 ( 3008) covalent geometry : angle 0.71038 ( 4111) *********************** 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 : 0.345 Fit side-chains REVERT: A 405 ASP cc_start: 0.8656 (m-30) cc_final: 0.8357 (m-30) REVERT: A 474 GLN cc_start: 0.6833 (tp-100) cc_final: 0.6477 (tp-100) REVERT: C 31 ASN cc_start: 0.9044 (m-40) cc_final: 0.8814 (m-40) REVERT: C 49 TYR cc_start: 0.6261 (m-10) cc_final: 0.5943 (m-10) REVERT: B 27 LEU cc_start: 0.6267 (tp) cc_final: 0.6017 (tp) REVERT: B 45 LEU cc_start: 0.8604 (mt) cc_final: 0.8181 (mt) REVERT: B 46 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7945 (mm-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1649 time to fit residues: 10.9084 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 : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3058 r_free = 0.3058 target = 0.060917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.050720 restraints weight = 11646.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.052565 restraints weight = 6937.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.053919 restraints weight = 4709.602| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1793 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= 0.190 Angle : 0.722 10.063 4124 Z= 0.380 Chirality : 0.048 0.163 452 Planarity : 0.006 0.084 540 Dihedral : 6.107 29.640 463 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.39), residues: 397 helix: -3.22 (0.77), residues: 34 sheet: -1.22 (0.49), residues: 114 loop : -2.59 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 107 HIS 0.002 0.001 HIS A 519 PHE 0.010 0.001 PHE A 342 TYR 0.021 0.002 TYR A 489 ARG 0.003 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 1) link_NAG-ASN : angle 0.78119 ( 3) hydrogen bonds : bond 0.04282 ( 86) hydrogen bonds : angle 5.77215 ( 222) SS BOND : bond 0.00895 ( 5) SS BOND : angle 1.97539 ( 10) covalent geometry : bond 0.00431 ( 3008) covalent geometry : angle 0.71638 ( 4111) *********************** 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 : 0.308 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8658 (m-30) cc_final: 0.8296 (m-30) REVERT: A 406 GLU cc_start: 0.9104 (pt0) cc_final: 0.8886 (pt0) REVERT: A 474 GLN cc_start: 0.6933 (tp-100) cc_final: 0.6560 (tp-100) REVERT: B 27 LEU cc_start: 0.6290 (tp) cc_final: 0.5841 (tp) REVERT: B 45 LEU cc_start: 0.8701 (mt) cc_final: 0.8243 (mt) REVERT: B 46 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7944 (mm-30) REVERT: B 98 ASP cc_start: 0.7597 (m-30) cc_final: 0.7397 (m-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1698 time to fit residues: 11.0806 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 : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3017 r_free = 0.3017 target = 0.059174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.049393 restraints weight = 12161.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.051164 restraints weight = 7190.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.052441 restraints weight = 4904.750| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 3014 Z= 0.278 Angle : 0.791 11.782 4124 Z= 0.411 Chirality : 0.049 0.172 452 Planarity : 0.006 0.068 540 Dihedral : 6.286 25.170 463 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.86 % Favored : 85.14 % Rotamer: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.38), residues: 397 helix: -3.12 (0.80), residues: 34 sheet: -1.28 (0.48), residues: 109 loop : -2.61 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 107 HIS 0.004 0.002 HIS A 519 PHE 0.011 0.002 PHE A 347 TYR 0.016 0.002 TYR B 33 ARG 0.005 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 1) link_NAG-ASN : angle 1.07090 ( 3) hydrogen bonds : bond 0.04358 ( 86) hydrogen bonds : angle 5.76187 ( 222) SS BOND : bond 0.00976 ( 5) SS BOND : angle 2.22013 ( 10) covalent geometry : bond 0.00631 ( 3008) covalent geometry : angle 0.78366 ( 4111) *********************** 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 : 0.292 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8729 (m-30) cc_final: 0.8353 (m-30) REVERT: A 406 GLU cc_start: 0.9021 (pt0) cc_final: 0.8782 (pt0) REVERT: C 31 ASN cc_start: 0.9138 (m-40) cc_final: 0.8919 (m-40) REVERT: B 27 LEU cc_start: 0.6484 (tp) cc_final: 0.6070 (tp) REVERT: B 45 LEU cc_start: 0.8651 (mt) cc_final: 0.8075 (mt) REVERT: B 46 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7797 (mm-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2004 time to fit residues: 12.4929 Evaluate side-chains 42 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 15 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3073 r_free = 0.3073 target = 0.060998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.051295 restraints weight = 11692.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.053066 restraints weight = 7112.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.054396 restraints weight = 4853.589| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3014 Z= 0.153 Angle : 0.716 10.161 4124 Z= 0.373 Chirality : 0.047 0.179 452 Planarity : 0.005 0.059 540 Dihedral : 5.694 24.379 463 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.39), residues: 397 helix: -3.34 (0.75), residues: 34 sheet: -1.35 (0.47), residues: 118 loop : -2.37 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.015 0.001 PHE A 342 TYR 0.015 0.001 TYR A 453 ARG 0.005 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 1) link_NAG-ASN : angle 0.70985 ( 3) hydrogen bonds : bond 0.03807 ( 86) hydrogen bonds : angle 5.74418 ( 222) SS BOND : bond 0.00958 ( 5) SS BOND : angle 1.96799 ( 10) covalent geometry : bond 0.00348 ( 3008) covalent geometry : angle 0.71019 ( 4111) *********************** 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 : 0.334 Fit side-chains REVERT: A 386 LYS cc_start: 0.8427 (mtmm) cc_final: 0.8136 (mtmm) REVERT: A 405 ASP cc_start: 0.8702 (m-30) cc_final: 0.8299 (m-30) REVERT: A 406 GLU cc_start: 0.8942 (pt0) cc_final: 0.8656 (pt0) REVERT: B 27 LEU cc_start: 0.6407 (tp) cc_final: 0.5934 (tp) REVERT: B 45 LEU cc_start: 0.8607 (mt) cc_final: 0.8123 (mt) REVERT: B 46 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7872 (mm-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1497 time to fit residues: 9.7766 Evaluate side-chains 42 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 9 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 28 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.061459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.051421 restraints weight = 12069.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.053287 restraints weight = 7043.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.054756 restraints weight = 4719.100| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3014 Z= 0.143 Angle : 0.690 8.531 4124 Z= 0.359 Chirality : 0.046 0.155 452 Planarity : 0.005 0.054 540 Dihedral : 5.471 24.227 463 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.40), residues: 397 helix: -3.39 (0.72), residues: 34 sheet: -1.35 (0.47), residues: 118 loop : -2.25 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 36 HIS 0.001 0.001 HIS A 519 PHE 0.013 0.001 PHE A 342 TYR 0.013 0.001 TYR A 453 ARG 0.003 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 1) link_NAG-ASN : angle 0.58822 ( 3) hydrogen bonds : bond 0.03637 ( 86) hydrogen bonds : angle 5.77756 ( 222) SS BOND : bond 0.00867 ( 5) SS BOND : angle 2.18536 ( 10) covalent geometry : bond 0.00327 ( 3008) covalent geometry : angle 0.68277 ( 4111) *********************** 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 : 0.333 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8375 (mtmm) cc_final: 0.7915 (mtmm) REVERT: A 405 ASP cc_start: 0.8654 (m-30) cc_final: 0.8311 (m-30) REVERT: A 406 GLU cc_start: 0.9071 (pt0) cc_final: 0.8717 (pt0) REVERT: A 474 GLN cc_start: 0.6787 (tp-100) cc_final: 0.6541 (tp-100) REVERT: C 31 ASN cc_start: 0.8730 (m-40) cc_final: 0.8457 (m110) REVERT: B 27 LEU cc_start: 0.6464 (tp) cc_final: 0.5981 (tp) REVERT: B 45 LEU cc_start: 0.8657 (mt) cc_final: 0.8183 (mt) REVERT: B 98 ASP cc_start: 0.7853 (m-30) cc_final: 0.6924 (m-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1538 time to fit residues: 10.0207 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 : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.0370 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 15 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3109 r_free = 0.3109 target = 0.062381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.052205 restraints weight = 11898.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.054088 restraints weight = 6937.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055560 restraints weight = 4633.933| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3014 Z= 0.139 Angle : 0.693 8.001 4124 Z= 0.359 Chirality : 0.046 0.155 452 Planarity : 0.005 0.053 540 Dihedral : 5.424 22.917 463 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.39), residues: 397 helix: -3.51 (0.67), residues: 34 sheet: -1.33 (0.47), residues: 113 loop : -2.20 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 107 HIS 0.002 0.001 HIS A 519 PHE 0.012 0.001 PHE A 342 TYR 0.013 0.001 TYR B 33 ARG 0.008 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 1) link_NAG-ASN : angle 0.48742 ( 3) hydrogen bonds : bond 0.03533 ( 86) hydrogen bonds : angle 5.52554 ( 222) SS BOND : bond 0.00802 ( 5) SS BOND : angle 1.98027 ( 10) covalent geometry : bond 0.00321 ( 3008) covalent geometry : angle 0.68705 ( 4111) *********************** 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 56 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8445 (mtmm) cc_final: 0.7878 (mtmm) REVERT: A 405 ASP cc_start: 0.8688 (m-30) cc_final: 0.8320 (m-30) REVERT: A 406 GLU cc_start: 0.8864 (pt0) cc_final: 0.8486 (pt0) REVERT: A 474 GLN cc_start: 0.6980 (tp-100) cc_final: 0.6665 (tp-100) REVERT: C 31 ASN cc_start: 0.8753 (m-40) cc_final: 0.8448 (m110) REVERT: B 45 LEU cc_start: 0.8640 (mt) cc_final: 0.8152 (mt) REVERT: B 46 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7933 (mm-30) REVERT: B 98 ASP cc_start: 0.7526 (m-30) cc_final: 0.7183 (m-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1545 time to fit residues: 10.7284 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 : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 5 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.061564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.051654 restraints weight = 11735.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.053491 restraints weight = 6936.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.054892 restraints weight = 4673.737| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3014 Z= 0.169 Angle : 0.713 8.510 4124 Z= 0.371 Chirality : 0.047 0.153 452 Planarity : 0.005 0.051 540 Dihedral : 5.507 24.778 463 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.40), residues: 397 helix: -3.43 (0.70), residues: 34 sheet: -1.39 (0.47), residues: 113 loop : -2.21 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 36 HIS 0.002 0.002 HIS A 519 PHE 0.015 0.001 PHE A 347 TYR 0.014 0.001 TYR A 453 ARG 0.004 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00047 ( 1) link_NAG-ASN : angle 0.43753 ( 3) hydrogen bonds : bond 0.03820 ( 86) hydrogen bonds : angle 5.59454 ( 222) SS BOND : bond 0.00841 ( 5) SS BOND : angle 2.23890 ( 10) covalent geometry : bond 0.00388 ( 3008) covalent geometry : angle 0.70568 ( 4111) *********************** 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 : 0.343 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8395 (mtmm) cc_final: 0.7824 (mtmm) REVERT: A 405 ASP cc_start: 0.8632 (m-30) cc_final: 0.8284 (m-30) REVERT: A 406 GLU cc_start: 0.8922 (pt0) cc_final: 0.8569 (pt0) REVERT: A 474 GLN cc_start: 0.6910 (tp-100) cc_final: 0.6595 (tp-100) REVERT: B 46 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7943 (mm-30) REVERT: B 98 ASP cc_start: 0.7474 (m-30) cc_final: 0.7221 (m-30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1334 time to fit residues: 8.7328 Evaluate side-chains 42 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.062098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.052312 restraints weight = 11645.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.054093 restraints weight = 7018.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.055429 restraints weight = 4788.560| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3014 Z= 0.140 Angle : 0.689 8.759 4124 Z= 0.357 Chirality : 0.046 0.139 452 Planarity : 0.005 0.053 540 Dihedral : 5.413 23.133 463 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.40), residues: 397 helix: -3.45 (0.67), residues: 34 sheet: -1.25 (0.48), residues: 113 loop : -2.16 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.011 0.001 PHE A 342 TYR 0.014 0.001 TYR A 453 ARG 0.004 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 1) link_NAG-ASN : angle 0.22923 ( 3) hydrogen bonds : bond 0.03588 ( 86) hydrogen bonds : angle 5.58616 ( 222) SS BOND : bond 0.00780 ( 5) SS BOND : angle 2.02970 ( 10) covalent geometry : bond 0.00323 ( 3008) covalent geometry : angle 0.68311 ( 4111) *********************** 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 53 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8470 (mtmm) cc_final: 0.7881 (mtmm) REVERT: A 405 ASP cc_start: 0.8669 (m-30) cc_final: 0.8336 (m-30) REVERT: A 406 GLU cc_start: 0.8845 (pt0) cc_final: 0.8512 (pt0) REVERT: A 474 GLN cc_start: 0.6856 (tp-100) cc_final: 0.6583 (tp-100) REVERT: C 31 ASN cc_start: 0.8447 (m110) cc_final: 0.8226 (m110) REVERT: B 45 LEU cc_start: 0.8573 (mt) cc_final: 0.8051 (mt) REVERT: B 104 MET cc_start: 0.7520 (tpp) cc_final: 0.7081 (tpp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1680 time to fit residues: 11.1204 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 : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.0070 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.0020 chunk 29 optimal weight: 0.0670 chunk 24 optimal weight: 10.0000 overall best weight: 0.2744 ------------------------------------------------------------------------------- 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 = 0.3132 r_free = 0.3132 target = 0.063375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.053215 restraints weight = 11685.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.055040 restraints weight = 6987.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.056097 restraints weight = 4747.834| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3014 Z= 0.114 Angle : 0.666 9.225 4124 Z= 0.343 Chirality : 0.045 0.155 452 Planarity : 0.004 0.049 540 Dihedral : 5.309 25.705 463 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.40), residues: 397 helix: -3.47 (0.65), residues: 34 sheet: -1.17 (0.48), residues: 113 loop : -2.07 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 107 HIS 0.001 0.001 HIS A 519 PHE 0.010 0.001 PHE A 377 TYR 0.011 0.001 TYR A 453 ARG 0.004 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 1) link_NAG-ASN : angle 0.33106 ( 3) hydrogen bonds : bond 0.03262 ( 86) hydrogen bonds : angle 5.40340 ( 222) SS BOND : bond 0.00707 ( 5) SS BOND : angle 1.82802 ( 10) covalent geometry : bond 0.00266 ( 3008) covalent geometry : angle 0.66039 ( 4111) ********************** 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 56 residues out of total 340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8424 (mtmm) cc_final: 0.7858 (mtmm) REVERT: A 405 ASP cc_start: 0.8648 (m-30) cc_final: 0.8356 (m-30) REVERT: A 406 GLU cc_start: 0.9026 (pt0) cc_final: 0.8719 (pt0) REVERT: A 474 GLN cc_start: 0.6909 (tp-100) cc_final: 0.6525 (tp-100) REVERT: C 31 ASN cc_start: 0.8317 (m110) cc_final: 0.8079 (m110) REVERT: B 45 LEU cc_start: 0.8639 (mt) cc_final: 0.8042 (mt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1601 time to fit residues: 10.9646 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 : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 5 optimal weight: 0.0030 chunk 7 optimal weight: 0.6980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.3111 r_free = 0.3111 target = 0.062397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.052368 restraints weight = 11673.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.054164 restraints weight = 7019.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.055192 restraints weight = 4784.082| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3014 Z= 0.144 Angle : 0.691 9.491 4124 Z= 0.356 Chirality : 0.046 0.153 452 Planarity : 0.004 0.051 540 Dihedral : 5.271 23.739 463 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.40), residues: 397 helix: -3.37 (0.69), residues: 34 sheet: -1.14 (0.48), residues: 113 loop : -2.05 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.010 0.001 PHE A 342 TYR 0.012 0.001 TYR A 453 ARG 0.004 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 1) link_NAG-ASN : angle 0.28817 ( 3) hydrogen bonds : bond 0.03709 ( 86) hydrogen bonds : angle 5.40973 ( 222) SS BOND : bond 0.00731 ( 5) SS BOND : angle 1.98732 ( 10) covalent geometry : bond 0.00332 ( 3008) covalent geometry : angle 0.68472 ( 4111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1440.36 seconds wall clock time: 25 minutes 32.91 seconds (1532.91 seconds total)