Starting phenix.real_space_refine on Fri May 9 18:16:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpz_27644/05_2025/8dpz_27644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpz_27644/05_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_27644/05_2025/8dpz_27644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpz_27644/05_2025/8dpz_27644.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpz_27644/05_2025/8dpz_27644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpz_27644/05_2025/8dpz_27644.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.017 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 2.72, per 1000 atoms: 0.82 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: 0.72 Conformation dependent library (CDL) restraints added in 366.7 milliseconds 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: 0.40 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: 0.82 Time building geometry restraints manager: 0.88 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: 1.340 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.030 Find NCS groups from input model: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (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 TRP 0.012 0.002 TRP F 103 HIS 0.001 0.001 HIS B 519 PHE 0.037 0.003 PHE G 83 TYR 0.018 0.002 TYR G 49 ARG 0.006 0.001 ARG G 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 1) link_NAG-ASN : angle 2.27697 ( 3) link_BETA1-4 : bond 0.00751 ( 1) link_BETA1-4 : angle 1.33408 ( 3) hydrogen bonds : bond 0.24268 ( 104) hydrogen bonds : angle 10.69454 ( 324) SS BOND : bond 0.00146 ( 5) SS BOND : angle 0.64337 ( 10) covalent geometry : bond 0.00416 ( 3413) covalent geometry : angle 0.77180 ( 4642) *********************** 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 : 0.344 Fit side-chains REVERT: B 406 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7919 (mt-10) REVERT: B 417 LYS cc_start: 0.8402 (tppt) cc_final: 0.8171 (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: 0.2200 time to fit residues: 16.7006 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 : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.117241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097681 restraints weight = 5099.351| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.24 r_work: 0.3136 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3420 Z= 0.215 Angle : 0.640 6.446 4658 Z= 0.339 Chirality : 0.046 0.167 501 Planarity : 0.005 0.047 595 Dihedral : 5.320 23.782 510 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.83 % Allowed : 6.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.39), residues: 412 helix: -3.74 (0.53), residues: 28 sheet: 0.21 (0.47), residues: 140 loop : -1.67 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.024 0.003 PHE G 83 TYR 0.014 0.002 TYR B 453 ARG 0.003 0.001 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 1) link_NAG-ASN : angle 1.66356 ( 3) link_BETA1-4 : bond 0.00529 ( 1) link_BETA1-4 : angle 1.28912 ( 3) hydrogen bonds : bond 0.04720 ( 104) hydrogen bonds : angle 6.73598 ( 324) SS BOND : bond 0.00383 ( 5) SS BOND : angle 2.16497 ( 10) covalent geometry : bond 0.00502 ( 3413) covalent geometry : angle 0.63074 ( 4642) *********************** 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 63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.386 Fit side-chains REVERT: B 406 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8510 (mt-10) REVERT: F 48 ILE cc_start: 0.8559 (mm) cc_final: 0.8322 (mm) REVERT: F 100 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7860 (tm-30) outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 0.2222 time to fit residues: 15.5430 Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.116978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097888 restraints weight = 5043.923| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.17 r_work: 0.3149 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3420 Z= 0.175 Angle : 0.634 11.379 4658 Z= 0.326 Chirality : 0.047 0.167 501 Planarity : 0.005 0.044 595 Dihedral : 5.140 21.299 510 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.22 % Allowed : 8.61 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.40), residues: 412 helix: -3.37 (0.67), residues: 28 sheet: 0.15 (0.45), residues: 147 loop : -1.56 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.020 0.002 PHE G 83 TYR 0.011 0.001 TYR B 453 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 1) link_NAG-ASN : angle 1.54315 ( 3) link_BETA1-4 : bond 0.00370 ( 1) link_BETA1-4 : angle 1.14579 ( 3) hydrogen bonds : bond 0.03878 ( 104) hydrogen bonds : angle 5.99440 ( 324) SS BOND : bond 0.00906 ( 5) SS BOND : angle 1.64381 ( 10) covalent geometry : bond 0.00416 ( 3413) covalent geometry : angle 0.62820 ( 4642) *********************** 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 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.375 Fit side-chains REVERT: B 406 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8445 (mt-10) REVERT: B 417 LYS cc_start: 0.8654 (tppt) cc_final: 0.8340 (tptt) REVERT: F 48 ILE cc_start: 0.8567 (mm) cc_final: 0.8333 (mm) REVERT: F 100 ASP cc_start: 0.8846 (t0) cc_final: 0.8633 (t0) REVERT: F 100 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7747 (tm-30) outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.2188 time to fit residues: 15.5690 Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 525 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.118072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097675 restraints weight = 5154.015| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.35 r_work: 0.3143 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3420 Z= 0.149 Angle : 0.593 9.925 4658 Z= 0.306 Chirality : 0.046 0.165 501 Planarity : 0.004 0.044 595 Dihedral : 4.947 21.026 510 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.39 % Allowed : 10.83 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.40), residues: 412 helix: -3.01 (0.76), residues: 27 sheet: 0.17 (0.45), residues: 147 loop : -1.55 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.018 0.002 PHE G 83 TYR 0.009 0.001 TYR B 453 ARG 0.003 0.000 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 1) link_NAG-ASN : angle 1.41100 ( 3) link_BETA1-4 : bond 0.00301 ( 1) link_BETA1-4 : angle 1.08076 ( 3) hydrogen bonds : bond 0.03502 ( 104) hydrogen bonds : angle 5.67028 ( 324) SS BOND : bond 0.00764 ( 5) SS BOND : angle 1.37569 ( 10) covalent geometry : bond 0.00352 ( 3413) covalent geometry : angle 0.58863 ( 4642) *********************** 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 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.365 Fit side-chains REVERT: B 406 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8521 (mt-10) REVERT: B 417 LYS cc_start: 0.8683 (tppt) cc_final: 0.8276 (tppt) REVERT: F 100 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7592 (tm-30) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.1781 time to fit residues: 13.0892 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 : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 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 = 0.3544 r_free = 0.3544 target = 0.118606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.098143 restraints weight = 5102.212| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.38 r_work: 0.3145 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2055 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= 0.144 Angle : 0.583 9.046 4658 Z= 0.301 Chirality : 0.045 0.163 501 Planarity : 0.004 0.043 595 Dihedral : 4.873 20.574 510 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.61 % Allowed : 10.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.40), residues: 412 helix: -2.85 (0.80), residues: 27 sheet: -0.03 (0.46), residues: 135 loop : -1.42 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.017 0.002 PHE G 83 TYR 0.017 0.001 TYR F 100F ARG 0.002 0.000 ARG F 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 1) link_NAG-ASN : angle 1.35323 ( 3) link_BETA1-4 : bond 0.00314 ( 1) link_BETA1-4 : angle 1.02732 ( 3) hydrogen bonds : bond 0.03395 ( 104) hydrogen bonds : angle 5.51991 ( 324) SS BOND : bond 0.00735 ( 5) SS BOND : angle 1.27742 ( 10) covalent geometry : bond 0.00340 ( 3413) covalent geometry : angle 0.57953 ( 4642) *********************** 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: 13 poor density : 55 time to evaluate : 0.400 Fit side-chains REVERT: B 376 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8694 (p) REVERT: B 406 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8300 (mt-10) REVERT: B 417 LYS cc_start: 0.8640 (tppt) cc_final: 0.8216 (tppt) REVERT: F 82 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7740 (mp) REVERT: F 100 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7623 (tm-30) outliers start: 13 outliers final: 6 residues processed: 63 average time/residue: 0.1924 time to fit residues: 14.6173 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 : 0.352 ------------------------------------------------------------------------------- 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 21 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.117374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097357 restraints weight = 5235.305| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.31 r_work: 0.3133 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2154 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= 0.183 Angle : 0.619 9.270 4658 Z= 0.321 Chirality : 0.046 0.175 501 Planarity : 0.004 0.043 595 Dihedral : 5.032 21.088 510 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.61 % Allowed : 10.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.40), residues: 412 helix: -2.88 (0.80), residues: 27 sheet: -0.11 (0.46), residues: 135 loop : -1.53 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 94 HIS 0.001 0.001 HIS B 519 PHE 0.019 0.002 PHE G 83 TYR 0.017 0.001 TYR F 100F ARG 0.002 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 1.47172 ( 3) link_BETA1-4 : bond 0.00253 ( 1) link_BETA1-4 : angle 1.05946 ( 3) hydrogen bonds : bond 0.03535 ( 104) hydrogen bonds : angle 5.51556 ( 324) SS BOND : bond 0.00838 ( 5) SS BOND : angle 1.39451 ( 10) covalent geometry : bond 0.00432 ( 3413) covalent geometry : angle 0.61520 ( 4642) *********************** 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 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.342 Fit side-chains REVERT: B 376 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8741 (p) REVERT: B 406 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 417 LYS cc_start: 0.8666 (tppt) cc_final: 0.8273 (tppt) REVERT: F 82 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7851 (mp) REVERT: F 100 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7732 (tm-30) outliers start: 13 outliers final: 8 residues processed: 61 average time/residue: 0.1804 time to fit residues: 13.2026 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 : 0.370 ------------------------------------------------------------------------------- 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 21 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 F residue 110 THR 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 26 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 0.0010 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098878 restraints weight = 5097.348| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.27 r_work: 0.3157 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 0.040 3420 Z= 0.138 Angle : 0.580 8.513 4658 Z= 0.302 Chirality : 0.046 0.167 501 Planarity : 0.004 0.043 595 Dihedral : 4.870 21.280 510 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.50 % Allowed : 12.50 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.40), residues: 412 helix: -2.62 (0.98), residues: 21 sheet: -0.03 (0.47), residues: 137 loop : -1.50 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 94 HIS 0.000 0.000 HIS B 519 PHE 0.017 0.002 PHE G 83 TYR 0.017 0.001 TYR F 100F ARG 0.002 0.000 ARG F 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 1) link_NAG-ASN : angle 1.30841 ( 3) link_BETA1-4 : bond 0.00277 ( 1) link_BETA1-4 : angle 0.99131 ( 3) hydrogen bonds : bond 0.03338 ( 104) hydrogen bonds : angle 5.40731 ( 324) SS BOND : bond 0.00704 ( 5) SS BOND : angle 1.29668 ( 10) covalent geometry : bond 0.00324 ( 3413) covalent geometry : angle 0.57673 ( 4642) *********************** 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 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.362 Fit side-chains REVERT: B 376 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8721 (p) REVERT: B 406 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8201 (mt-10) REVERT: B 417 LYS cc_start: 0.8653 (tppt) cc_final: 0.8269 (tppt) REVERT: F 82 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7796 (mp) REVERT: F 100 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7641 (tm-30) outliers start: 9 outliers final: 6 residues processed: 61 average time/residue: 0.1994 time to fit residues: 14.4084 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 : 0.382 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 0.0670 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.118385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.098618 restraints weight = 5112.787| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.28 r_work: 0.3154 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2252 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= 0.147 Angle : 0.595 8.496 4658 Z= 0.307 Chirality : 0.046 0.161 501 Planarity : 0.004 0.042 595 Dihedral : 4.877 22.441 510 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.06 % Allowed : 13.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.40), residues: 412 helix: -2.79 (0.94), residues: 22 sheet: -0.05 (0.47), residues: 137 loop : -1.38 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 94 HIS 0.001 0.001 HIS B 519 PHE 0.017 0.002 PHE G 83 TYR 0.019 0.001 TYR F 100F ARG 0.003 0.000 ARG G 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 1) link_NAG-ASN : angle 1.30906 ( 3) link_BETA1-4 : bond 0.00275 ( 1) link_BETA1-4 : angle 0.99715 ( 3) hydrogen bonds : bond 0.03275 ( 104) hydrogen bonds : angle 5.41577 ( 324) SS BOND : bond 0.00732 ( 5) SS BOND : angle 1.35783 ( 10) covalent geometry : bond 0.00346 ( 3413) covalent geometry : angle 0.59140 ( 4642) *********************** 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 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.352 Fit side-chains REVERT: B 376 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8710 (p) REVERT: B 406 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8337 (mt-10) REVERT: B 417 LYS cc_start: 0.8652 (tppt) cc_final: 0.8271 (tppt) REVERT: F 82 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7796 (mp) REVERT: F 100 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7635 (tm-30) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.1963 time to fit residues: 14.9666 Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 21 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.0470 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.119727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.100017 restraints weight = 5065.408| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.25 r_work: 0.3176 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2293 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= 0.127 Angle : 0.581 8.069 4658 Z= 0.298 Chirality : 0.045 0.152 501 Planarity : 0.004 0.042 595 Dihedral : 4.816 24.874 510 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.22 % Allowed : 14.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.40), residues: 412 helix: -2.59 (0.98), residues: 22 sheet: -0.01 (0.47), residues: 137 loop : -1.26 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.016 0.001 PHE G 83 TYR 0.015 0.001 TYR F 100F ARG 0.002 0.000 ARG G 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00043 ( 1) link_NAG-ASN : angle 1.22434 ( 3) link_BETA1-4 : bond 0.00325 ( 1) link_BETA1-4 : angle 0.96794 ( 3) hydrogen bonds : bond 0.03115 ( 104) hydrogen bonds : angle 5.36101 ( 324) SS BOND : bond 0.00719 ( 5) SS BOND : angle 1.33627 ( 10) covalent geometry : bond 0.00298 ( 3413) covalent geometry : angle 0.57689 ( 4642) *********************** 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 63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.388 Fit side-chains REVERT: B 406 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8337 (mt-10) REVERT: B 417 LYS cc_start: 0.8631 (tppt) cc_final: 0.8249 (tppt) REVERT: F 82 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7797 (mp) REVERT: F 100 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7617 (tm-30) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.2017 time to fit residues: 14.4404 Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 68 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 26 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.117545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.098015 restraints weight = 5102.970| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.25 r_work: 0.3142 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2363 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= 0.188 Angle : 0.637 8.851 4658 Z= 0.326 Chirality : 0.046 0.174 501 Planarity : 0.004 0.042 595 Dihedral : 5.062 25.541 510 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.22 % Allowed : 15.00 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.40), residues: 412 helix: -2.90 (0.79), residues: 28 sheet: 0.02 (0.47), residues: 136 loop : -1.39 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 94 HIS 0.001 0.001 HIS B 519 PHE 0.019 0.002 PHE G 83 TYR 0.026 0.002 TYR F 59 ARG 0.007 0.001 ARG G 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 1) link_NAG-ASN : angle 1.43102 ( 3) link_BETA1-4 : bond 0.00282 ( 1) link_BETA1-4 : angle 1.03028 ( 3) hydrogen bonds : bond 0.03391 ( 104) hydrogen bonds : angle 5.43987 ( 324) SS BOND : bond 0.00754 ( 5) SS BOND : angle 1.46038 ( 10) covalent geometry : bond 0.00446 ( 3413) covalent geometry : angle 0.63269 ( 4642) ********************** 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 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.395 Fit side-chains REVERT: B 376 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8729 (p) REVERT: B 406 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8332 (mt-10) REVERT: B 417 LYS cc_start: 0.8678 (tppt) cc_final: 0.8305 (tppt) REVERT: F 82 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7826 (mp) REVERT: F 100 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7732 (tm-30) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 0.1985 time to fit residues: 13.6640 Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 68 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 37 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 0.0370 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 31 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.120485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100896 restraints weight = 5097.823| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.25 r_work: 0.3185 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3420 Z= 0.109 Angle : 0.566 7.562 4658 Z= 0.290 Chirality : 0.044 0.144 501 Planarity : 0.004 0.042 595 Dihedral : 4.779 27.062 510 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.22 % Allowed : 15.00 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.41), residues: 412 helix: -2.57 (0.96), residues: 22 sheet: 0.05 (0.48), residues: 137 loop : -1.22 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.016 0.001 PHE G 83 TYR 0.015 0.001 TYR F 100F ARG 0.007 0.000 ARG G 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00010 ( 1) link_NAG-ASN : angle 1.11135 ( 3) link_BETA1-4 : bond 0.00366 ( 1) link_BETA1-4 : angle 0.93386 ( 3) hydrogen bonds : bond 0.02973 ( 104) hydrogen bonds : angle 5.26018 ( 324) SS BOND : bond 0.00706 ( 5) SS BOND : angle 1.34623 ( 10) covalent geometry : bond 0.00252 ( 3413) covalent geometry : angle 0.56190 ( 4642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2239.87 seconds wall clock time: 39 minutes 22.59 seconds (2362.59 seconds total)