Starting phenix.real_space_refine on Fri Aug 22 13:36:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpz_27644/08_2025/8dpz_27644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpz_27644/08_2025/8dpz_27644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dpz_27644/08_2025/8dpz_27644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpz_27644/08_2025/8dpz_27644.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpz_27644/08_2025/8dpz_27644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpz_27644/08_2025/8dpz_27644.cif" } resolution = 3.38 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= -0.017 sd= 0.107 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 11 5.16 5 C 2115 2.51 5 N 551 2.21 5 O 649 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3326 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1480 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain breaks: 1 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 982 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.96, per 1000 atoms: 0.29 Number of scatterers: 3326 At special positions: 0 Unit cell: (71.28, 90.72, 74.52, 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 11 16.00 O 649 8.00 N 551 7.00 C 2115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 98.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 6 sheets defined 11.2% alpha, 39.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.210A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.822A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.608A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.959A pdb=" N THR F 87 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.535A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N GLU F 100H" --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 12.269A pdb=" N TYR F 98 " --> pdb=" O GLU F 100H" (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA F 100J" --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.535A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N GLU F 100H" --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 12.269A pdb=" N TYR F 98 " --> pdb=" O GLU F 100H" (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA F 100J" --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN F 33 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.623A pdb=" N GLN F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.536A pdb=" N ALA G 34 " --> pdb=" O GLN G 89 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR G 49 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 324 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: 0.32 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1045 1.34 - 1.46: 898 1.46 - 1.58: 1458 1.58 - 1.70: 0 1.70 - 1.81: 12 Bond restraints: 3413 Sorted by residual: bond pdb=" C GLU G 79 " pdb=" N PRO G 80 " ideal model delta sigma weight residual 1.334 1.351 -0.018 8.40e-03 1.42e+04 4.43e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C SER G 7 " pdb=" N PRO G 8 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.27e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.83e+00 bond pdb=" CB ASP F 100A" pdb=" CG ASP F 100A" ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.70e+00 ... (remaining 3408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 4413 1.63 - 3.26: 188 3.26 - 4.89: 31 4.89 - 6.51: 7 6.51 - 8.14: 3 Bond angle restraints: 4642 Sorted by residual: angle pdb=" C ASP G 50 " pdb=" N ALA G 51 " pdb=" CA ALA G 51 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.29e+00 angle pdb=" N ASP F 100 " pdb=" CA ASP F 100 " pdb=" C ASP F 100 " ideal model delta sigma weight residual 109.95 105.91 4.04 1.44e+00 4.82e-01 7.86e+00 angle pdb=" C ASN G 93 " pdb=" N TRP G 94 " pdb=" CA TRP G 94 " ideal model delta sigma weight residual 120.06 123.39 -3.33 1.19e+00 7.06e-01 7.81e+00 angle pdb=" C PHE G 83 " pdb=" CA PHE G 83 " pdb=" CB PHE G 83 " ideal model delta sigma weight residual 111.31 115.81 -4.50 1.68e+00 3.54e-01 7.18e+00 angle pdb=" N TRP G 94 " pdb=" CA TRP G 94 " pdb=" C TRP G 94 " ideal model delta sigma weight residual 113.57 117.12 -3.55 1.38e+00 5.25e-01 6.62e+00 ... (remaining 4637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 1822 16.50 - 33.01: 177 33.01 - 49.51: 25 49.51 - 66.02: 5 66.02 - 82.52: 4 Dihedral angle restraints: 2033 sinusoidal: 817 harmonic: 1216 Sorted by residual: dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual 93.00 56.65 36.35 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CA VAL F 95 " pdb=" C VAL F 95 " pdb=" N ALA F 96 " pdb=" CA ALA F 96 " ideal model delta harmonic sigma weight residual 180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASN G 93 " pdb=" C ASN G 93 " pdb=" N TRP G 94 " pdb=" CA TRP G 94 " ideal model delta harmonic sigma weight residual -180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 2030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 290 0.035 - 0.070: 137 0.070 - 0.106: 51 0.106 - 0.141: 19 0.141 - 0.176: 4 Chirality restraints: 501 Sorted by residual: chirality pdb=" CB THR G 102 " pdb=" CA THR G 102 " pdb=" OG1 THR G 102 " pdb=" CG2 THR G 102 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA TRP G 94 " pdb=" N TRP G 94 " pdb=" C TRP G 94 " pdb=" CB TRP G 94 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA ILE B 402 " pdb=" N ILE B 402 " pdb=" C ILE B 402 " pdb=" CB ILE B 402 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 498 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 79 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO G 80 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " 0.041 5.00e-02 4.00e+02 6.29e-02 6.34e+00 pdb=" N PRO B 337 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 83 " -0.014 2.00e-02 2.50e+03 1.57e-02 4.33e+00 pdb=" CG PHE G 83 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE G 83 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE G 83 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE G 83 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 83 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE G 83 " -0.001 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1186 2.87 - 3.38: 2663 3.38 - 3.89: 5282 3.89 - 4.39: 5920 4.39 - 4.90: 10828 Nonbonded interactions: 25879 Sorted by model distance: nonbonded pdb=" OH TYR F 97 " pdb=" OE1 GLU F 99 " model vdw 2.363 3.040 nonbonded pdb=" OD2 ASP B 405 " pdb=" OG SER G 30 " model vdw 2.408 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.420 3.120 nonbonded pdb=" OD1 ASP F 100 " pdb=" N ASP F 100A" model vdw 2.427 3.120 nonbonded pdb=" NH1 ARG G 61 " pdb=" OD2 ASP G 82 " model vdw 2.429 3.120 ... (remaining 25874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.030 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3420 Z= 0.188 Angle : 0.774 8.142 4658 Z= 0.412 Chirality : 0.050 0.176 501 Planarity : 0.007 0.069 595 Dihedral : 13.012 82.522 1248 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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 aren not related in a simple way. whole: -2.09 (0.38), residues: 412 helix: -4.20 (0.35), residues: 27 sheet: -0.08 (0.45), residues: 139 loop : -1.92 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 24 TYR 0.018 0.002 TYR G 49 PHE 0.037 0.003 PHE G 83 TRP 0.012 0.002 TRP F 103 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 3413) covalent geometry : angle 0.77180 ( 4642) SS BOND : bond 0.00146 ( 5) SS BOND : angle 0.64337 ( 10) hydrogen bonds : bond 0.24268 ( 104) hydrogen bonds : angle 10.69454 ( 324) link_BETA1-4 : bond 0.00751 ( 1) link_BETA1-4 : angle 1.33408 ( 3) link_NAG-ASN : bond 0.00387 ( 1) link_NAG-ASN : angle 2.27697 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.077 Fit side-chains REVERT: B 406 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7917 (mt-10) REVERT: B 417 LYS cc_start: 0.8402 (tppt) cc_final: 0.8168 (tptt) REVERT: F 48 ILE cc_start: 0.8306 (mm) cc_final: 0.7982 (mm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0841 time to fit residues: 6.4174 Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.119483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.100194 restraints weight = 5127.858| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.20 r_work: 0.3177 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3420 Z= 0.149 Angle : 0.582 5.460 4658 Z= 0.309 Chirality : 0.044 0.155 501 Planarity : 0.005 0.052 595 Dihedral : 5.127 24.704 510 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % 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 aren not related in a simple way. whole: -1.58 (0.40), residues: 412 helix: -3.72 (0.53), residues: 28 sheet: 0.29 (0.47), residues: 140 loop : -1.60 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 454 TYR 0.012 0.001 TYR F 100F PHE 0.020 0.002 PHE G 83 TRP 0.013 0.002 TRP G 94 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3413) covalent geometry : angle 0.57436 ( 4642) SS BOND : bond 0.00390 ( 5) SS BOND : angle 1.82334 ( 10) hydrogen bonds : bond 0.04068 ( 104) hydrogen bonds : angle 6.65568 ( 324) link_BETA1-4 : bond 0.00330 ( 1) link_BETA1-4 : angle 1.21036 ( 3) link_NAG-ASN : bond 0.00043 ( 1) link_NAG-ASN : angle 1.49181 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.138 Fit side-chains REVERT: B 406 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8525 (mt-10) REVERT: B 417 LYS cc_start: 0.8615 (tppt) cc_final: 0.8335 (tptt) REVERT: F 48 ILE cc_start: 0.8537 (mm) cc_final: 0.8308 (mm) REVERT: F 100 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7788 (tm-30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0825 time to fit residues: 5.8270 Evaluate side-chains 56 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.0470 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.119479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.100284 restraints weight = 5103.929| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.18 r_work: 0.3183 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3420 Z= 0.133 Angle : 0.585 11.568 4658 Z= 0.304 Chirality : 0.045 0.151 501 Planarity : 0.004 0.046 595 Dihedral : 4.877 21.767 510 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.83 % Allowed : 8.61 % Favored : 90.56 % 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 aren not related in a simple way. whole: -1.38 (0.40), residues: 412 helix: -3.22 (0.68), residues: 28 sheet: 0.23 (0.45), residues: 148 loop : -1.41 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.013 0.001 TYR F 100F PHE 0.018 0.002 PHE G 83 TRP 0.012 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3413) covalent geometry : angle 0.58102 ( 4642) SS BOND : bond 0.00764 ( 5) SS BOND : angle 1.41531 ( 10) hydrogen bonds : bond 0.03710 ( 104) hydrogen bonds : angle 5.93109 ( 324) link_BETA1-4 : bond 0.00355 ( 1) link_BETA1-4 : angle 1.06684 ( 3) link_NAG-ASN : bond 0.00009 ( 1) link_NAG-ASN : angle 1.33875 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.127 Fit side-chains REVERT: B 417 LYS cc_start: 0.8614 (tppt) cc_final: 0.8296 (tppt) REVERT: F 100 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7607 (tm-30) outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.0860 time to fit residues: 5.9382 Evaluate side-chains 58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.0040 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.119241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.099610 restraints weight = 5063.856| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.28 r_work: 0.3166 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3420 Z= 0.137 Angle : 0.583 9.586 4658 Z= 0.300 Chirality : 0.046 0.156 501 Planarity : 0.004 0.047 595 Dihedral : 4.780 20.459 510 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.39 % Allowed : 11.11 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.40), residues: 412 helix: -2.57 (0.93), residues: 21 sheet: 0.24 (0.45), residues: 148 loop : -1.46 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 18 TYR 0.016 0.001 TYR F 100F PHE 0.016 0.002 PHE F 78 TRP 0.011 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3413) covalent geometry : angle 0.57929 ( 4642) SS BOND : bond 0.00751 ( 5) SS BOND : angle 1.29102 ( 10) hydrogen bonds : bond 0.03424 ( 104) hydrogen bonds : angle 5.62131 ( 324) link_BETA1-4 : bond 0.00306 ( 1) link_BETA1-4 : angle 1.06231 ( 3) link_NAG-ASN : bond 0.00053 ( 1) link_NAG-ASN : angle 1.36955 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.081 Fit side-chains REVERT: B 347 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7599 (m-10) REVERT: B 417 LYS cc_start: 0.8626 (tppt) cc_final: 0.8261 (tppt) REVERT: F 100 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7605 (tm-30) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 0.0880 time to fit residues: 6.1211 Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.118636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.099039 restraints weight = 5137.620| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.24 r_work: 0.3160 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3420 Z= 0.153 Angle : 0.586 9.098 4658 Z= 0.303 Chirality : 0.046 0.162 501 Planarity : 0.004 0.046 595 Dihedral : 4.794 20.492 510 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.89 % Allowed : 10.56 % Favored : 85.56 % 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 aren not related in a simple way. whole: -1.25 (0.40), residues: 412 helix: -2.47 (0.97), residues: 21 sheet: 0.24 (0.45), residues: 148 loop : -1.41 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 18 TYR 0.014 0.001 TYR F 100F PHE 0.017 0.002 PHE F 78 TRP 0.011 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 3413) covalent geometry : angle 0.58170 ( 4642) SS BOND : bond 0.00728 ( 5) SS BOND : angle 1.33964 ( 10) hydrogen bonds : bond 0.03391 ( 104) hydrogen bonds : angle 5.47293 ( 324) link_BETA1-4 : bond 0.00314 ( 1) link_BETA1-4 : angle 1.06975 ( 3) link_NAG-ASN : bond 0.00096 ( 1) link_NAG-ASN : angle 1.37563 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.101 Fit side-chains REVERT: B 347 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.7668 (m-10) REVERT: B 376 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8753 (p) REVERT: B 417 LYS cc_start: 0.8650 (tppt) cc_final: 0.8263 (tppt) REVERT: F 100 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7653 (tm-30) outliers start: 14 outliers final: 6 residues processed: 63 average time/residue: 0.0674 time to fit residues: 5.0553 Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.118992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098795 restraints weight = 5127.156| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.36 r_work: 0.3154 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3420 Z= 0.143 Angle : 0.581 8.682 4658 Z= 0.300 Chirality : 0.045 0.158 501 Planarity : 0.004 0.046 595 Dihedral : 4.770 20.276 510 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.50 % Allowed : 11.67 % Favored : 85.83 % 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 aren not related in a simple way. whole: -1.39 (0.40), residues: 412 helix: -2.49 (0.96), residues: 21 sheet: 0.04 (0.46), residues: 136 loop : -1.38 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 18 TYR 0.017 0.001 TYR F 100F PHE 0.016 0.002 PHE F 78 TRP 0.010 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3413) covalent geometry : angle 0.57700 ( 4642) SS BOND : bond 0.00730 ( 5) SS BOND : angle 1.35178 ( 10) hydrogen bonds : bond 0.03305 ( 104) hydrogen bonds : angle 5.35146 ( 324) link_BETA1-4 : bond 0.00308 ( 1) link_BETA1-4 : angle 1.04357 ( 3) link_NAG-ASN : bond 0.00080 ( 1) link_NAG-ASN : angle 1.35336 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.127 Fit side-chains REVERT: B 347 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7562 (m-10) REVERT: B 417 LYS cc_start: 0.8573 (tppt) cc_final: 0.8142 (tppt) REVERT: B 418 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7579 (mt) REVERT: F 82 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7646 (mp) REVERT: F 100 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7575 (tm-30) outliers start: 9 outliers final: 5 residues processed: 60 average time/residue: 0.0704 time to fit residues: 5.0536 Evaluate side-chains 63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.117794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097989 restraints weight = 5230.414| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.30 r_work: 0.3139 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3420 Z= 0.177 Angle : 0.619 9.024 4658 Z= 0.318 Chirality : 0.046 0.173 501 Planarity : 0.004 0.044 595 Dihedral : 4.947 21.615 510 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.61 % Allowed : 11.11 % Favored : 85.28 % 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 aren not related in a simple way. whole: -1.48 (0.40), residues: 412 helix: -2.53 (0.97), residues: 21 sheet: -0.04 (0.47), residues: 135 loop : -1.42 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.017 0.001 TYR F 100F PHE 0.017 0.002 PHE F 78 TRP 0.010 0.002 TRP G 94 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 3413) covalent geometry : angle 0.61406 ( 4642) SS BOND : bond 0.00750 ( 5) SS BOND : angle 1.45090 ( 10) hydrogen bonds : bond 0.03436 ( 104) hydrogen bonds : angle 5.40446 ( 324) link_BETA1-4 : bond 0.00278 ( 1) link_BETA1-4 : angle 1.08580 ( 3) link_NAG-ASN : bond 0.00225 ( 1) link_NAG-ASN : angle 1.55327 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.097 Fit side-chains REVERT: B 347 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.7703 (m-10) REVERT: B 376 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8733 (p) REVERT: B 417 LYS cc_start: 0.8641 (tppt) cc_final: 0.8205 (tppt) REVERT: F 100 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7766 (tm-30) outliers start: 13 outliers final: 7 residues processed: 63 average time/residue: 0.0777 time to fit residues: 5.8215 Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 0.0670 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.119363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099725 restraints weight = 5185.776| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.27 r_work: 0.3169 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3420 Z= 0.130 Angle : 0.588 8.259 4658 Z= 0.302 Chirality : 0.045 0.157 501 Planarity : 0.004 0.043 595 Dihedral : 4.866 24.257 510 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.50 % Allowed : 13.89 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.40), residues: 412 helix: -2.86 (0.91), residues: 22 sheet: 0.01 (0.47), residues: 137 loop : -1.30 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 50 TYR 0.015 0.001 TYR F 100F PHE 0.015 0.001 PHE F 78 TRP 0.011 0.001 TRP G 94 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3413) covalent geometry : angle 0.58356 ( 4642) SS BOND : bond 0.00724 ( 5) SS BOND : angle 1.38314 ( 10) hydrogen bonds : bond 0.03236 ( 104) hydrogen bonds : angle 5.37774 ( 324) link_BETA1-4 : bond 0.00291 ( 1) link_BETA1-4 : angle 0.98612 ( 3) link_NAG-ASN : bond 0.00057 ( 1) link_NAG-ASN : angle 1.29272 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.077 Fit side-chains REVERT: B 347 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.7609 (m-10) REVERT: B 376 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8736 (p) REVERT: B 417 LYS cc_start: 0.8619 (tppt) cc_final: 0.8200 (tppt) REVERT: B 418 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7802 (mt) REVERT: F 82 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7709 (mp) REVERT: F 100 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7654 (tm-30) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 0.0771 time to fit residues: 5.4906 Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 0.0030 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.3568 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.120971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.101524 restraints weight = 5110.702| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.23 r_work: 0.3196 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3420 Z= 0.108 Angle : 0.559 7.599 4658 Z= 0.287 Chirality : 0.044 0.143 501 Planarity : 0.004 0.043 595 Dihedral : 4.681 25.986 510 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.50 % Allowed : 14.44 % Favored : 83.06 % 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 aren not related in a simple way. whole: -1.29 (0.40), residues: 412 helix: -2.51 (0.97), residues: 22 sheet: -0.16 (0.46), residues: 143 loop : -1.12 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 50 TYR 0.010 0.001 TYR F 100F PHE 0.014 0.001 PHE F 78 TRP 0.012 0.001 TRP G 94 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 3413) covalent geometry : angle 0.55505 ( 4642) SS BOND : bond 0.00699 ( 5) SS BOND : angle 1.29711 ( 10) hydrogen bonds : bond 0.02945 ( 104) hydrogen bonds : angle 5.23726 ( 324) link_BETA1-4 : bond 0.00383 ( 1) link_BETA1-4 : angle 0.95661 ( 3) link_NAG-ASN : bond 0.00013 ( 1) link_NAG-ASN : angle 1.15646 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.126 Fit side-chains REVERT: B 417 LYS cc_start: 0.8600 (tppt) cc_final: 0.8182 (tppt) REVERT: B 418 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7708 (mt) REVERT: F 82 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7719 (mp) REVERT: F 100 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7622 (tm-30) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 0.0876 time to fit residues: 6.2152 Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.100375 restraints weight = 5145.922| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.28 r_work: 0.3172 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3420 Z= 0.141 Angle : 0.608 8.053 4658 Z= 0.308 Chirality : 0.045 0.152 501 Planarity : 0.004 0.042 595 Dihedral : 4.825 26.015 510 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.06 % Allowed : 13.61 % Favored : 83.33 % 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 aren not related in a simple way. whole: -1.27 (0.41), residues: 412 helix: -2.49 (0.97), residues: 22 sheet: -0.15 (0.47), residues: 143 loop : -1.10 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 18 TYR 0.024 0.001 TYR F 59 PHE 0.016 0.002 PHE F 78 TRP 0.010 0.001 TRP G 94 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3413) covalent geometry : angle 0.60479 ( 4642) SS BOND : bond 0.00711 ( 5) SS BOND : angle 1.33000 ( 10) hydrogen bonds : bond 0.03124 ( 104) hydrogen bonds : angle 5.27241 ( 324) link_BETA1-4 : bond 0.00299 ( 1) link_BETA1-4 : angle 0.97233 ( 3) link_NAG-ASN : bond 0.00077 ( 1) link_NAG-ASN : angle 1.30141 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.107 Fit side-chains REVERT: B 347 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7514 (m-10) REVERT: B 376 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8722 (p) REVERT: B 417 LYS cc_start: 0.8629 (tppt) cc_final: 0.8212 (tppt) REVERT: B 418 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7811 (mt) REVERT: F 82 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7915 (mp) REVERT: F 100 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: G 18 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.8309 (mmm160) outliers start: 11 outliers final: 6 residues processed: 60 average time/residue: 0.0905 time to fit residues: 6.3213 Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.121038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.101332 restraints weight = 5167.652| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.27 r_work: 0.3189 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3420 Z= 0.117 Angle : 0.577 8.436 4658 Z= 0.291 Chirality : 0.044 0.144 501 Planarity : 0.004 0.043 595 Dihedral : 4.714 26.960 510 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.78 % Allowed : 13.61 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.41), residues: 412 helix: -2.19 (1.04), residues: 22 sheet: -0.11 (0.47), residues: 143 loop : -1.08 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 18 TYR 0.013 0.001 TYR F 100F PHE 0.014 0.001 PHE F 78 TRP 0.011 0.001 TRP G 94 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3413) covalent geometry : angle 0.57351 ( 4642) SS BOND : bond 0.00703 ( 5) SS BOND : angle 1.30093 ( 10) hydrogen bonds : bond 0.02946 ( 104) hydrogen bonds : angle 5.18598 ( 324) link_BETA1-4 : bond 0.00301 ( 1) link_BETA1-4 : angle 0.92809 ( 3) link_NAG-ASN : bond 0.00007 ( 1) link_NAG-ASN : angle 1.17067 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1012.57 seconds wall clock time: 17 minutes 58.22 seconds (1078.22 seconds total)