Starting phenix.real_space_refine on Fri Aug 22 13:40:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eqf_28537/08_2025/8eqf_28537.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eqf_28537/08_2025/8eqf_28537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eqf_28537/08_2025/8eqf_28537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eqf_28537/08_2025/8eqf_28537.map" model { file = "/net/cci-nas-00/data/ceres_data/8eqf_28537/08_2025/8eqf_28537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eqf_28537/08_2025/8eqf_28537.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 2133 2.51 5 N 556 2.21 5 O 644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 3348 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: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 97} Chain: "B" 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: 0.76, per 1000 atoms: 0.23 Number of scatterers: 3348 At special positions: 0 Unit cell: (54.516, 64.428, 108.206, 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 644 8.00 N 556 7.00 C 2133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 481 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 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 B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 336 " Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 76.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 9.5% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.772A pdb=" N VAL A 334 " --> pdb=" O PRO A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.509A pdb=" N TRP A 346 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 removed outlier: 4.421A pdb=" N ARG A 401 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 415 removed outlier: 3.529A pdb=" N TYR A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.980A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.986A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.083A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 351 Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 355 removed outlier: 6.928A pdb=" N CYS A 354 " --> pdb=" O CYS A 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.837A pdb=" N GLY H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.062A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.510A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 100 hydrogen bonds defined for protein. 243 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: 0.39 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1058 1.34 - 1.46: 917 1.46 - 1.58: 1445 1.58 - 1.70: 0 1.70 - 1.81: 18 Bond restraints: 3438 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.439 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" CA ASN A 433 " pdb=" CB ASN A 433 " ideal model delta sigma weight residual 1.530 1.514 0.015 1.43e-02 4.89e+03 1.14e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.05e+00 ... (remaining 3433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 4397 1.09 - 2.18: 227 2.18 - 3.27: 34 3.27 - 4.36: 15 4.36 - 5.45: 1 Bond angle restraints: 4674 Sorted by residual: angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 114.17 110.43 3.74 1.14e+00 7.69e-01 1.07e+01 angle pdb=" C ASP A 357 " pdb=" CA ASP A 357 " pdb=" CB ASP A 357 " ideal model delta sigma weight residual 110.78 114.52 -3.74 1.60e+00 3.91e-01 5.45e+00 angle pdb=" N LEU A 434 " pdb=" CA LEU A 434 " pdb=" CB LEU A 434 " ideal model delta sigma weight residual 114.27 110.50 3.77 1.64e+00 3.72e-01 5.30e+00 angle pdb=" CA ASP A 357 " pdb=" CB ASP A 357 " pdb=" CG ASP A 357 " ideal model delta sigma weight residual 112.60 114.65 -2.05 1.00e+00 1.00e+00 4.21e+00 angle pdb=" C ASN A 433 " pdb=" CA ASN A 433 " pdb=" CB ASN A 433 " ideal model delta sigma weight residual 109.75 112.89 -3.14 1.65e+00 3.67e-01 3.62e+00 ... (remaining 4669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.00: 1916 23.00 - 46.00: 103 46.00 - 69.00: 13 69.00 - 92.00: 2 92.00 - 115.00: 3 Dihedral angle restraints: 2037 sinusoidal: 813 harmonic: 1224 Sorted by residual: dihedral pdb=" CB CYS A 384 " pdb=" SG CYS A 384 " pdb=" SG CYS A 518 " pdb=" CB CYS A 518 " ideal model delta sinusoidal sigma weight residual 93.00 133.02 -40.02 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" C2 NAG B 2 " pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " pdb=" C5 NAG B 2 " ideal model delta sinusoidal sigma weight residual -62.96 52.04 -115.00 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C1 NAG B 2 " pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " pdb=" C6 NAG B 2 " ideal model delta sinusoidal sigma weight residual 171.16 -78.51 -110.33 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 2034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 307 0.034 - 0.068: 143 0.068 - 0.102: 27 0.102 - 0.136: 19 0.136 - 0.170: 4 Chirality restraints: 500 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 336 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA ILE A 427 " pdb=" N ILE A 427 " pdb=" C ILE A 427 " pdb=" CB ILE A 427 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 497 not shown) Planarity restraints: 602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 357 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" CG ASP A 357 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP A 357 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 357 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 336 " -0.013 2.00e-02 2.50e+03 1.27e-02 2.01e+00 pdb=" CG ASN A 336 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 336 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 336 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 357 " 0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C ASP A 357 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP A 357 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR A 358 " 0.007 2.00e-02 2.50e+03 ... (remaining 599 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 30 2.58 - 3.16: 2736 3.16 - 3.74: 4913 3.74 - 4.32: 7512 4.32 - 4.90: 12547 Nonbonded interactions: 27738 Sorted by model distance: nonbonded pdb=" O4 NAG B 1 " pdb=" O6 NAG B 2 " model vdw 1.998 3.040 nonbonded pdb=" O3 NAG B 1 " pdb=" O7 NAG B 1 " model vdw 2.012 3.040 nonbonded pdb=" O ASP H 62 " pdb=" OG SER H 63 " model vdw 2.038 3.040 nonbonded pdb=" O ASP A 357 " pdb=" OD1 ASP A 357 " model vdw 2.142 3.040 nonbonded pdb=" OH TYR A 482 " pdb=" O TYR L 92 " model vdw 2.289 3.040 ... (remaining 27733 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: 10.310 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.340 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.005 0.070 3446 Z= 0.222 Angle : 0.598 7.350 4692 Z= 0.322 Chirality : 0.043 0.170 500 Planarity : 0.003 0.026 601 Dihedral : 14.570 115.000 1247 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.38 (0.42), residues: 416 helix: -4.44 (0.43), residues: 27 sheet: -0.01 (0.44), residues: 136 loop : 0.23 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.011 0.001 TYR H 95 PHE 0.008 0.001 PHE A 393 TRP 0.011 0.002 TRP A 429 HIS 0.002 0.001 HIS L 100 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 3438) covalent geometry : angle 0.57064 ( 4674) SS BOND : bond 0.00297 ( 6) SS BOND : angle 0.73804 ( 12) hydrogen bonds : bond 0.15502 ( 100) hydrogen bonds : angle 7.83945 ( 243) link_BETA1-4 : bond 0.00357 ( 1) link_BETA1-4 : angle 4.39639 ( 3) link_NAG-ASN : bond 0.01145 ( 1) link_NAG-ASN : angle 5.54637 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.120 Fit side-chains REVERT: A 436 SER cc_start: 0.8112 (m) cc_final: 0.7883 (m) REVERT: A 488 TYR cc_start: 0.8303 (m-80) cc_final: 0.7914 (m-80) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0714 time to fit residues: 4.5159 Evaluate side-chains 50 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN H 57 ASN L 30 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.096570 restraints weight = 5206.068| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.01 r_work: 0.3056 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 3446 Z= 0.327 Angle : 0.735 10.868 4692 Z= 0.360 Chirality : 0.050 0.221 500 Planarity : 0.005 0.032 601 Dihedral : 6.991 45.954 513 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.38 % Allowed : 5.25 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.37 (0.41), residues: 416 helix: -4.57 (0.40), residues: 27 sheet: 0.20 (0.45), residues: 134 loop : 0.12 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 87 TYR 0.015 0.002 TYR A 362 PHE 0.013 0.002 PHE A 393 TRP 0.016 0.002 TRP A 429 HIS 0.002 0.001 HIS L 30 Details of bonding type rmsd covalent geometry : bond 0.00758 ( 3438) covalent geometry : angle 0.69618 ( 4674) SS BOND : bond 0.00441 ( 6) SS BOND : angle 1.01558 ( 12) hydrogen bonds : bond 0.04395 ( 100) hydrogen bonds : angle 6.92649 ( 243) link_BETA1-4 : bond 0.00153 ( 1) link_BETA1-4 : angle 5.16192 ( 3) link_NAG-ASN : bond 0.01317 ( 1) link_NAG-ASN : angle 7.62986 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.125 Fit side-chains REVERT: H 115 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7956 (mm110) REVERT: L 81 GLU cc_start: 0.7684 (pm20) cc_final: 0.7471 (pm20) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.0594 time to fit residues: 4.2083 Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.0470 chunk 3 optimal weight: 0.1980 chunk 7 optimal weight: 0.3980 chunk 21 optimal weight: 0.0970 chunk 10 optimal weight: 0.3980 chunk 17 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.0770 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 overall best weight: 0.1234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.098931 restraints weight = 5140.013| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.01 r_work: 0.3099 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3446 Z= 0.124 Angle : 0.566 8.049 4692 Z= 0.283 Chirality : 0.043 0.156 500 Planarity : 0.003 0.031 601 Dihedral : 6.091 45.058 513 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.10 % Allowed : 6.08 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.23 (0.41), residues: 416 helix: -4.44 (0.45), residues: 27 sheet: 0.07 (0.44), residues: 136 loop : 0.37 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.010 0.001 TYR A 501 PHE 0.008 0.001 PHE L 98 TRP 0.013 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3438) covalent geometry : angle 0.54099 ( 4674) SS BOND : bond 0.00181 ( 6) SS BOND : angle 0.66558 ( 12) hydrogen bonds : bond 0.03466 ( 100) hydrogen bonds : angle 6.56247 ( 243) link_BETA1-4 : bond 0.00050 ( 1) link_BETA1-4 : angle 2.99302 ( 3) link_NAG-ASN : bond 0.00866 ( 1) link_NAG-ASN : angle 5.85705 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.075 Fit side-chains REVERT: A 488 TYR cc_start: 0.8369 (m-80) cc_final: 0.7897 (m-80) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 0.0539 time to fit residues: 4.0318 Evaluate side-chains 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 470 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.0060 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 0.0970 chunk 40 optimal weight: 0.0270 chunk 1 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 overall best weight: 0.1252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN L 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.108980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099684 restraints weight = 5062.882| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.98 r_work: 0.3116 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3446 Z= 0.121 Angle : 0.546 7.024 4692 Z= 0.276 Chirality : 0.043 0.163 500 Planarity : 0.003 0.032 601 Dihedral : 5.582 43.756 513 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.38 % Allowed : 8.56 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.15 (0.42), residues: 416 helix: -4.00 (0.71), residues: 20 sheet: 0.31 (0.45), residues: 136 loop : 0.47 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 87 TYR 0.014 0.001 TYR A 501 PHE 0.007 0.001 PHE L 98 TRP 0.012 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3438) covalent geometry : angle 0.52807 ( 4674) SS BOND : bond 0.00182 ( 6) SS BOND : angle 0.66261 ( 12) hydrogen bonds : bond 0.03247 ( 100) hydrogen bonds : angle 6.24556 ( 243) link_BETA1-4 : bond 0.00077 ( 1) link_BETA1-4 : angle 2.64188 ( 3) link_NAG-ASN : bond 0.01027 ( 1) link_NAG-ASN : angle 4.83105 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.086 Fit side-chains REVERT: A 488 TYR cc_start: 0.8404 (m-80) cc_final: 0.7879 (m-80) outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.0581 time to fit residues: 3.7853 Evaluate side-chains 50 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 470 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 0.0030 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 21 optimal weight: 0.0670 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.0770 chunk 29 optimal weight: 0.1980 overall best weight: 0.1486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.108986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099416 restraints weight = 5106.678| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.05 r_work: 0.3105 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3446 Z= 0.127 Angle : 0.527 6.405 4692 Z= 0.269 Chirality : 0.043 0.166 500 Planarity : 0.003 0.034 601 Dihedral : 5.253 44.090 513 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.83 % Allowed : 9.39 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.18 (0.42), residues: 416 helix: -3.99 (0.73), residues: 20 sheet: 0.42 (0.45), residues: 136 loop : 0.43 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.016 0.001 TYR A 501 PHE 0.007 0.001 PHE L 98 TRP 0.012 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3438) covalent geometry : angle 0.51144 ( 4674) SS BOND : bond 0.00238 ( 6) SS BOND : angle 0.67703 ( 12) hydrogen bonds : bond 0.03154 ( 100) hydrogen bonds : angle 6.13578 ( 243) link_BETA1-4 : bond 0.00053 ( 1) link_BETA1-4 : angle 2.40639 ( 3) link_NAG-ASN : bond 0.00965 ( 1) link_NAG-ASN : angle 4.33428 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.085 Fit side-chains REVERT: A 488 TYR cc_start: 0.8433 (m-80) cc_final: 0.8018 (m-80) outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.0679 time to fit residues: 4.3292 Evaluate side-chains 50 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.0970 chunk 21 optimal weight: 0.0770 chunk 23 optimal weight: 0.4980 chunk 26 optimal weight: 0.2980 chunk 6 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 0.0570 chunk 28 optimal weight: 0.4980 overall best weight: 0.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.108639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.099289 restraints weight = 5072.950| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.98 r_work: 0.3108 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3446 Z= 0.158 Angle : 0.545 6.216 4692 Z= 0.280 Chirality : 0.043 0.167 500 Planarity : 0.004 0.035 601 Dihedral : 5.253 44.654 513 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.83 % Allowed : 10.50 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.10 (0.41), residues: 416 helix: -3.96 (0.75), residues: 20 sheet: 0.47 (0.45), residues: 130 loop : 0.30 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.018 0.001 TYR A 501 PHE 0.008 0.001 PHE A 393 TRP 0.014 0.002 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3438) covalent geometry : angle 0.53099 ( 4674) SS BOND : bond 0.00241 ( 6) SS BOND : angle 0.70973 ( 12) hydrogen bonds : bond 0.03281 ( 100) hydrogen bonds : angle 6.12006 ( 243) link_BETA1-4 : bond 0.00189 ( 1) link_BETA1-4 : angle 2.28959 ( 3) link_NAG-ASN : bond 0.00990 ( 1) link_NAG-ASN : angle 4.15733 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.120 Fit side-chains REVERT: A 488 TYR cc_start: 0.8473 (m-80) cc_final: 0.8057 (m-80) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.0656 time to fit residues: 4.0817 Evaluate side-chains 48 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 13 optimal weight: 0.0010 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 20 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 0.0770 chunk 0 optimal weight: 0.4980 overall best weight: 0.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.098513 restraints weight = 5194.489| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.05 r_work: 0.3093 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3446 Z= 0.188 Angle : 0.562 6.201 4692 Z= 0.288 Chirality : 0.044 0.169 500 Planarity : 0.004 0.035 601 Dihedral : 5.341 45.732 513 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.93 % Allowed : 9.67 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.10 (0.41), residues: 416 helix: -4.28 (0.57), residues: 27 sheet: 0.46 (0.45), residues: 130 loop : 0.25 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.021 0.001 TYR A 501 PHE 0.009 0.001 PHE A 393 TRP 0.013 0.002 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 3438) covalent geometry : angle 0.54880 ( 4674) SS BOND : bond 0.00268 ( 6) SS BOND : angle 0.75610 ( 12) hydrogen bonds : bond 0.03368 ( 100) hydrogen bonds : angle 6.25151 ( 243) link_BETA1-4 : bond 0.00306 ( 1) link_BETA1-4 : angle 2.19205 ( 3) link_NAG-ASN : bond 0.01031 ( 1) link_NAG-ASN : angle 4.13350 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.142 Fit side-chains REVERT: A 488 TYR cc_start: 0.8490 (m-80) cc_final: 0.8119 (m-80) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.0564 time to fit residues: 3.7673 Evaluate side-chains 53 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 64 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 8 optimal weight: 0.0270 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 15 optimal weight: 0.0570 chunk 3 optimal weight: 0.0170 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 overall best weight: 0.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.099797 restraints weight = 5169.069| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.03 r_work: 0.3111 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3446 Z= 0.112 Angle : 0.519 5.183 4692 Z= 0.268 Chirality : 0.042 0.165 500 Planarity : 0.003 0.034 601 Dihedral : 5.102 43.730 513 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.55 % Allowed : 11.33 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.06 (0.42), residues: 416 helix: -3.78 (0.71), residues: 26 sheet: 0.52 (0.45), residues: 130 loop : 0.33 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 87 TYR 0.018 0.001 TYR A 501 PHE 0.008 0.001 PHE L 98 TRP 0.012 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 3438) covalent geometry : angle 0.50817 ( 4674) SS BOND : bond 0.00223 ( 6) SS BOND : angle 0.62231 ( 12) hydrogen bonds : bond 0.03089 ( 100) hydrogen bonds : angle 6.01307 ( 243) link_BETA1-4 : bond 0.00037 ( 1) link_BETA1-4 : angle 2.24160 ( 3) link_NAG-ASN : bond 0.00890 ( 1) link_NAG-ASN : angle 3.50014 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.076 Fit side-chains REVERT: A 348 ARG cc_start: 0.8587 (ttm170) cc_final: 0.8332 (ttm170) REVERT: A 488 TYR cc_start: 0.8455 (m-80) cc_final: 0.8078 (m-80) REVERT: L 56 SER cc_start: 0.8562 (t) cc_final: 0.8328 (p) outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.0562 time to fit residues: 3.5971 Evaluate side-chains 50 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.0970 chunk 30 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 8 optimal weight: 0.0040 chunk 14 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 overall best weight: 0.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.108520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.099165 restraints weight = 5135.555| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.99 r_work: 0.3103 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3446 Z= 0.179 Angle : 0.547 5.631 4692 Z= 0.283 Chirality : 0.044 0.168 500 Planarity : 0.004 0.045 601 Dihedral : 5.249 45.121 513 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.66 % Allowed : 11.05 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.02 (0.41), residues: 416 helix: -3.77 (0.71), residues: 26 sheet: 0.45 (0.45), residues: 130 loop : 0.26 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.024 0.001 TYR A 501 PHE 0.009 0.001 PHE A 393 TRP 0.014 0.002 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 3438) covalent geometry : angle 0.53556 ( 4674) SS BOND : bond 0.00267 ( 6) SS BOND : angle 0.79757 ( 12) hydrogen bonds : bond 0.03313 ( 100) hydrogen bonds : angle 6.10544 ( 243) link_BETA1-4 : bond 0.00194 ( 1) link_BETA1-4 : angle 1.99120 ( 3) link_NAG-ASN : bond 0.01015 ( 1) link_NAG-ASN : angle 3.72195 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.153 Fit side-chains REVERT: A 488 TYR cc_start: 0.8496 (m-80) cc_final: 0.8140 (m-80) REVERT: H 53 TYR cc_start: 0.8246 (p90) cc_final: 0.7908 (p90) outliers start: 6 outliers final: 5 residues processed: 51 average time/residue: 0.0710 time to fit residues: 4.4426 Evaluate side-chains 52 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.3980 chunk 13 optimal weight: 0.0060 chunk 14 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 40 optimal weight: 0.0980 chunk 35 optimal weight: 0.0980 chunk 16 optimal weight: 0.1980 chunk 38 optimal weight: 0.1980 overall best weight: 0.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.100153 restraints weight = 5038.113| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.00 r_work: 0.3120 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3446 Z= 0.115 Angle : 0.514 4.947 4692 Z= 0.266 Chirality : 0.042 0.165 500 Planarity : 0.003 0.034 601 Dihedral : 5.018 43.334 513 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.66 % Allowed : 10.77 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.02 (0.41), residues: 416 helix: -3.80 (0.70), residues: 26 sheet: 0.48 (0.45), residues: 130 loop : 0.30 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.020 0.001 TYR A 501 PHE 0.007 0.001 PHE L 98 TRP 0.013 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3438) covalent geometry : angle 0.50400 ( 4674) SS BOND : bond 0.00189 ( 6) SS BOND : angle 0.66344 ( 12) hydrogen bonds : bond 0.03058 ( 100) hydrogen bonds : angle 5.97335 ( 243) link_BETA1-4 : bond 0.00026 ( 1) link_BETA1-4 : angle 2.06723 ( 3) link_NAG-ASN : bond 0.00914 ( 1) link_NAG-ASN : angle 3.32773 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.128 Fit side-chains REVERT: A 348 ARG cc_start: 0.8584 (ttm170) cc_final: 0.8317 (ttm170) REVERT: A 482 TYR cc_start: 0.8370 (m-80) cc_final: 0.8126 (m-10) REVERT: A 488 TYR cc_start: 0.8430 (m-80) cc_final: 0.8064 (m-80) REVERT: H 34 MET cc_start: 0.8505 (mmt) cc_final: 0.8296 (mmt) REVERT: H 53 TYR cc_start: 0.8134 (p90) cc_final: 0.7905 (p90) REVERT: L 56 SER cc_start: 0.8535 (t) cc_final: 0.8310 (p) outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 0.0650 time to fit residues: 4.3645 Evaluate side-chains 51 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 64 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 33 optimal weight: 0.0970 chunk 13 optimal weight: 0.0000 chunk 8 optimal weight: 0.0170 chunk 30 optimal weight: 0.1980 chunk 18 optimal weight: 0.0980 chunk 27 optimal weight: 0.4980 chunk 29 optimal weight: 0.0870 chunk 34 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 overall best weight: 0.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN L 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.110463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101159 restraints weight = 5173.435| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.01 r_work: 0.3141 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3446 Z= 0.090 Angle : 0.495 4.626 4692 Z= 0.257 Chirality : 0.042 0.164 500 Planarity : 0.003 0.033 601 Dihedral : 4.804 40.995 513 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.10 % Allowed : 11.88 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.06 (0.41), residues: 416 helix: -3.77 (0.71), residues: 26 sheet: 0.53 (0.45), residues: 130 loop : 0.32 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 87 TYR 0.019 0.001 TYR A 501 PHE 0.006 0.001 PHE L 98 TRP 0.011 0.001 TRP A 429 HIS 0.001 0.000 HIS L 100 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 3438) covalent geometry : angle 0.48600 ( 4674) SS BOND : bond 0.00180 ( 6) SS BOND : angle 0.65754 ( 12) hydrogen bonds : bond 0.02907 ( 100) hydrogen bonds : angle 5.76559 ( 243) link_BETA1-4 : bond 0.00145 ( 1) link_BETA1-4 : angle 1.97049 ( 3) link_NAG-ASN : bond 0.00895 ( 1) link_NAG-ASN : angle 3.09459 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1226.06 seconds wall clock time: 21 minutes 44.87 seconds (1304.87 seconds total)