Starting phenix.real_space_refine on Thu Oct 22 18:24:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22pd_68583/10_2026/22pd_68583.cif Found real_map, /net/cci-nas-00/data/ceres_data/22pd_68583/10_2026/22pd_68583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22pd_68583/10_2026/22pd_68583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22pd_68583/10_2026/22pd_68583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22pd_68583/10_2026/22pd_68583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22pd_68583/10_2026/22pd_68583.map" } resolution = 2.95 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= 0.005 sd= 0.034 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 2139 2.51 5 N 573 2.21 5 O 651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3378 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 993 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 124} Chain: "B" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106} Chain: "C" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1519 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.08, per 1000 atoms: 0.32 Number of scatterers: 3378 At special positions: 0 Unit cell: (61.7025, 101.755, 89.8475, 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 651 8.00 N 573 7.00 C 2139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.07 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 100.1 milliseconds 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 794 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 10.1% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.689A pdb=" N THR A 90 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.937A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.541A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.798A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 59 removed outlier: 3.868A pdb=" N THR A 56 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 33 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.694A pdb=" N THR B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS B 23 " --> pdb=" O PHE B 71 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.519A pdb=" N LEU B 11 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 105 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.519A pdb=" N LEU B 11 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 105 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.557A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 474 95 hydrogen bonds defined for protein. 237 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: 0.47 Time building geometry restraints manager: 0.29 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: 1088 1.34 - 1.46: 938 1.46 - 1.58: 1419 1.58 - 1.70: 0 1.70 - 1.82: 17 Bond restraints: 3462 Sorted by residual: bond pdb=" N CYS C 379 " pdb=" CA CYS C 379 " ideal model delta sigma weight residual 1.452 1.501 -0.049 1.41e-02 5.03e+03 1.19e+01 bond pdb=" N TYR C 380 " pdb=" CA TYR C 380 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.37e+00 bond pdb=" C LYS C 424 " pdb=" N LEU C 425 " ideal model delta sigma weight residual 1.333 1.397 -0.065 2.74e-02 1.33e+03 5.61e+00 bond pdb=" C LYS C 378 " pdb=" N CYS C 379 " ideal model delta sigma weight residual 1.328 1.353 -0.025 1.61e-02 3.86e+03 2.45e+00 bond pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 1.516 1.491 0.025 1.80e-02 3.09e+03 2.00e+00 ... (remaining 3457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 4523 1.87 - 3.75: 154 3.75 - 5.62: 17 5.62 - 7.49: 12 7.49 - 9.36: 2 Bond angle restraints: 4708 Sorted by residual: angle pdb=" C CYS C 525 " pdb=" N GLY C 526 " pdb=" CA GLY C 526 " ideal model delta sigma weight residual 121.70 114.96 6.74 1.80e+00 3.09e-01 1.40e+01 angle pdb=" C CYS C 379 " pdb=" CA CYS C 379 " pdb=" CB CYS C 379 " ideal model delta sigma weight residual 113.45 106.26 7.19 1.98e+00 2.55e-01 1.32e+01 angle pdb=" C LYS B 107 " pdb=" N ARG B 108 " pdb=" CA ARG B 108 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C GLY A 54 " pdb=" N ASP A 55 " pdb=" CA ASP A 55 " ideal model delta sigma weight residual 121.54 127.79 -6.25 1.91e+00 2.74e-01 1.07e+01 angle pdb=" CA TYR C 380 " pdb=" C TYR C 380 " pdb=" O TYR C 380 " ideal model delta sigma weight residual 120.51 115.87 4.64 1.43e+00 4.89e-01 1.06e+01 ... (remaining 4703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.16: 1792 14.16 - 28.32: 174 28.32 - 42.48: 53 42.48 - 56.64: 14 56.64 - 70.79: 4 Dihedral angle restraints: 2037 sinusoidal: 782 harmonic: 1255 Sorted by residual: dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual -86.00 -35.49 -50.51 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CA THR B 109 " pdb=" C THR B 109 " pdb=" N VAL B 110 " pdb=" CA VAL B 110 " ideal model delta harmonic sigma weight residual -180.00 -151.20 -28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ALA C 372 " pdb=" C ALA C 372 " pdb=" N PRO C 373 " pdb=" CA PRO C 373 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 2034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 295 0.034 - 0.068: 144 0.068 - 0.102: 40 0.102 - 0.136: 24 0.136 - 0.170: 6 Chirality restraints: 509 Sorted by residual: chirality pdb=" CB ILE C 472 " pdb=" CA ILE C 472 " pdb=" CG1 ILE C 472 " pdb=" CG2 ILE C 472 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CB THR B 109 " pdb=" CA THR B 109 " pdb=" OG1 THR B 109 " pdb=" CG2 THR B 109 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ALA C 372 " pdb=" N ALA C 372 " pdb=" C ALA C 372 " pdb=" CB ALA C 372 " both_signs ideal model delta sigma weight residual False 2.48 2.34 0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 506 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 378 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C LYS C 378 " 0.057 2.00e-02 2.50e+03 pdb=" O LYS C 378 " -0.021 2.00e-02 2.50e+03 pdb=" N CYS C 379 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 111 " 0.052 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO A 112 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 525 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C CYS C 525 " 0.031 2.00e-02 2.50e+03 pdb=" O CYS C 525 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY C 526 " -0.011 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 76 2.66 - 3.22: 3278 3.22 - 3.78: 5110 3.78 - 4.34: 7083 4.34 - 4.90: 11591 Nonbonded interactions: 27138 Sorted by model distance: nonbonded pdb=" NH1 ARG B 108 " pdb=" O THR B 109 " model vdw 2.097 3.120 nonbonded pdb=" O ASP B 82 " pdb=" OH TYR B 86 " model vdw 2.176 3.040 nonbonded pdb=" OH TYR A 33 " pdb=" O VAL C 503 " model vdw 2.177 3.040 nonbonded pdb=" O ALA B 13 " pdb=" N LYS B 107 " model vdw 2.204 3.120 nonbonded pdb=" NE2 GLN C 474 " pdb=" O LYS C 478 " model vdw 2.207 3.120 ... (remaining 27133 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.010 Find NCS groups from input model: 0.030 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:7.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 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 0.065 3469 Z= 0.227 Angle : 0.847 9.364 4723 Z= 0.460 Chirality : 0.048 0.170 509 Planarity : 0.005 0.080 611 Dihedral : 12.666 70.793 1225 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.28 % Allowed : 0.56 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.39), residues: 428 helix: -3.23 (0.79), residues: 20 sheet: -0.74 (0.44), residues: 128 loop : -1.67 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG B 108 TYR 0.012 0.002 TYR C 501 PHE 0.021 0.002 PHE C 371 TRP 0.018 0.002 TRP C 353 HIS 0.001 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.23 ( 3462) covalent geometry : angle 0.82774 / 0.45 ( 4708) SS BOND : bond 0.01478 / 0.73 ( 6) SS BOND : angle 3.44144 / 1.40 ( 12) hydrogen bonds : bond 0.24048 / 15.20 ( 92) hydrogen bonds : angle 9.29082 / 6.35 ( 237) link_NAG-ASN : bond 0.00250 / 0.13 ( 1) link_NAG-ASN : angle 2.73347 / 1.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 GLN cc_start: 0.8628 (mm110) cc_final: 0.8386 (mm-40) REVERT: B 27 GLN cc_start: 0.7280 (mm-40) cc_final: 0.6992 (mm-40) REVERT: C 440 LYS cc_start: 0.8589 (tptp) cc_final: 0.8315 (tptp) outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.4494 time to fit residues: 35.8807 Evaluate side-chains 61 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 371 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.092837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.081736 restraints weight = 11758.891| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 4.50 r_work: 0.3452 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 3469 Z= 0.291 Angle : 0.848 10.227 4723 Z= 0.433 Chirality : 0.051 0.176 509 Planarity : 0.006 0.054 611 Dihedral : 6.447 26.004 506 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.19 % Allowed : 13.69 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.39), residues: 428 helix: -3.34 (0.64), residues: 34 sheet: -0.79 (0.42), residues: 138 loop : -1.74 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 24 TYR 0.017 0.002 TYR A 79 PHE 0.019 0.002 PHE C 377 TRP 0.016 0.002 TRP A 106 HIS 0.001 0.000 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.29 ( 3462) covalent geometry : angle 0.83589 / 0.43 ( 4708) SS BOND : bond 0.01208 / 0.62 ( 6) SS BOND : angle 2.66559 / 1.34 ( 12) hydrogen bonds : bond 0.04713 / 3.24 ( 92) hydrogen bonds : angle 6.59657 / 4.52 ( 237) link_NAG-ASN : bond 0.00326 / 0.17 ( 1) link_NAG-ASN : angle 2.54842 / 1.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.7676 (m-80) cc_final: 0.7325 (m-10) REVERT: A 81 GLU cc_start: 0.8337 (pp20) cc_final: 0.8102 (pp20) REVERT: A 120 GLN cc_start: 0.8958 (mm110) cc_final: 0.8709 (mm110) REVERT: C 440 LYS cc_start: 0.8705 (tptp) cc_final: 0.8463 (tptp) outliers start: 15 outliers final: 7 residues processed: 77 average time/residue: 0.4177 time to fit residues: 33.3700 Evaluate side-chains 63 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [38, 6, 36, 15, 1, 2, 19, 5, 37, 25, 8] chunk 38 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.095901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.084698 restraints weight = 11262.760| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 4.44 r_work: 0.3510 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3469 Z= 0.157 Angle : 0.738 10.322 4723 Z= 0.368 Chirality : 0.047 0.183 509 Planarity : 0.004 0.048 611 Dihedral : 5.617 26.168 504 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.75 % Allowed : 18.44 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.40), residues: 428 helix: -2.05 (1.11), residues: 22 sheet: -0.52 (0.44), residues: 138 loop : -1.42 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 24 TYR 0.013 0.001 TYR A 79 PHE 0.012 0.001 PHE C 377 TRP 0.008 0.001 TRP C 436 HIS 0.001 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 3462) covalent geometry : angle 0.72735 / 0.36 ( 4708) SS BOND : bond 0.00974 / 0.50 ( 6) SS BOND : angle 2.29878 / 1.17 ( 12) hydrogen bonds : bond 0.04025 / 2.72 ( 92) hydrogen bonds : angle 6.23259 / 4.26 ( 237) link_NAG-ASN : bond 0.00198 / 0.10 ( 1) link_NAG-ASN : angle 2.43071 / 1.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLN cc_start: 0.8961 (mm110) cc_final: 0.8698 (mm-40) REVERT: B 38 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8574 (tm-30) REVERT: C 406 GLU cc_start: 0.8650 (pt0) cc_final: 0.8282 (pm20) REVERT: C 440 LYS cc_start: 0.8695 (tptp) cc_final: 0.8453 (tptp) REVERT: C 515 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8003 (p90) outliers start: 17 outliers final: 8 residues processed: 73 average time/residue: 0.3855 time to fit residues: 29.3014 Evaluate side-chains 63 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [29, 4, 26, 40, 20, 11, 5, 36, 39, 21, 12] chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.097885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.086556 restraints weight = 11247.004| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 4.53 r_work: 0.3550 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3469 Z= 0.123 Angle : 0.722 10.927 4723 Z= 0.353 Chirality : 0.046 0.171 509 Planarity : 0.004 0.045 611 Dihedral : 5.071 24.124 504 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.35 % Allowed : 21.23 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.39), residues: 428 helix: -2.61 (0.87), residues: 28 sheet: -0.05 (0.45), residues: 126 loop : -1.44 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 24 TYR 0.012 0.001 TYR B 49 PHE 0.015 0.001 PHE B 83 TRP 0.007 0.001 TRP A 36 HIS 0.001 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 3462) covalent geometry : angle 0.71597 / 0.35 ( 4708) SS BOND : bond 0.00704 / 0.40 ( 6) SS BOND : angle 1.70330 / 0.84 ( 12) hydrogen bonds : bond 0.03499 / 2.39 ( 92) hydrogen bonds : angle 5.96580 / 4.04 ( 237) link_NAG-ASN : bond 0.00105 / 0.06 ( 1) link_NAG-ASN : angle 2.22564 / 1.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9591 (mmp) cc_final: 0.9388 (mmm) REVERT: A 120 GLN cc_start: 0.8931 (mm110) cc_final: 0.8685 (mm-40) REVERT: C 392 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6362 (p90) REVERT: C 406 GLU cc_start: 0.8565 (pt0) cc_final: 0.8265 (pm20) REVERT: C 440 LYS cc_start: 0.8650 (tptp) cc_final: 0.8419 (tptp) REVERT: C 498 ARG cc_start: 0.8514 (tpp80) cc_final: 0.8205 (mmm160) outliers start: 12 outliers final: 7 residues processed: 69 average time/residue: 0.4376 time to fit residues: 31.2611 Evaluate side-chains 62 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [40, 38, 20, 24, 37, 26, 7, 13, 2, 31, 21] chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.098152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.086690 restraints weight = 11274.873| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 4.55 r_work: 0.3561 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3469 Z= 0.123 Angle : 0.716 11.842 4723 Z= 0.347 Chirality : 0.046 0.175 509 Planarity : 0.004 0.043 611 Dihedral : 4.922 25.721 504 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.19 % Allowed : 21.23 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.39), residues: 428 helix: -2.66 (0.83), residues: 28 sheet: 0.06 (0.47), residues: 114 loop : -1.28 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 24 TYR 0.009 0.001 TYR A 58 PHE 0.017 0.001 PHE B 83 TRP 0.008 0.001 TRP A 106 HIS 0.000 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 3462) covalent geometry : angle 0.71103 / 0.35 ( 4708) SS BOND : bond 0.00703 / 0.39 ( 6) SS BOND : angle 1.47941 / 0.78 ( 12) hydrogen bonds : bond 0.03471 / 2.37 ( 92) hydrogen bonds : angle 5.84522 / 3.94 ( 237) link_NAG-ASN : bond 0.00028 / 0.01 ( 1) link_NAG-ASN : angle 2.01179 / 1.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9626 (mmp) cc_final: 0.9313 (mmm) REVERT: A 120 GLN cc_start: 0.8946 (mm110) cc_final: 0.8719 (mm-40) REVERT: C 392 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6446 (p90) REVERT: C 406 GLU cc_start: 0.8537 (pt0) cc_final: 0.8266 (pm20) REVERT: C 440 LYS cc_start: 0.8618 (tptp) cc_final: 0.8386 (tptp) REVERT: C 460 ASN cc_start: 0.8524 (t0) cc_final: 0.8175 (t0) REVERT: C 515 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8107 (p90) outliers start: 15 outliers final: 8 residues processed: 73 average time/residue: 0.3891 time to fit residues: 29.6251 Evaluate side-chains 64 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [25, 15, 35, 23, 6, 5, 39, 32, 21, 34, 38] chunk 25 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.0670 chunk 5 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.095980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.084628 restraints weight = 11363.374| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 4.48 r_work: 0.3512 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3469 Z= 0.169 Angle : 0.768 12.336 4723 Z= 0.376 Chirality : 0.047 0.164 509 Planarity : 0.004 0.042 611 Dihedral : 5.182 25.788 504 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.75 % Allowed : 22.91 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.39), residues: 428 helix: -2.60 (0.86), residues: 28 sheet: -0.28 (0.45), residues: 126 loop : -1.09 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 498 TYR 0.014 0.001 TYR B 49 PHE 0.019 0.002 PHE B 83 TRP 0.006 0.001 TRP A 106 HIS 0.001 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 3462) covalent geometry : angle 0.76191 / 0.37 ( 4708) SS BOND : bond 0.00733 / 0.39 ( 6) SS BOND : angle 1.69515 / 0.88 ( 12) hydrogen bonds : bond 0.03706 / 2.52 ( 92) hydrogen bonds : angle 5.89397 / 3.97 ( 237) link_NAG-ASN : bond 0.00100 / 0.05 ( 1) link_NAG-ASN : angle 2.24330 / 1.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8719 (pm20) cc_final: 0.8514 (pm20) REVERT: A 120 GLN cc_start: 0.8900 (mm110) cc_final: 0.8688 (mm-40) REVERT: C 392 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6427 (p90) REVERT: C 406 GLU cc_start: 0.8553 (pt0) cc_final: 0.8181 (pm20) REVERT: C 440 LYS cc_start: 0.8645 (tptp) cc_final: 0.8328 (tptp) REVERT: C 515 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8121 (p90) outliers start: 17 outliers final: 11 residues processed: 73 average time/residue: 0.4201 time to fit residues: 31.7612 Evaluate side-chains 68 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [22, 18, 12, 15, 10, 6, 26, 37, 29, 19, 9] chunk 22 optimal weight: 0.2980 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.094786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.083403 restraints weight = 11495.567| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 4.49 r_work: 0.3491 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3469 Z= 0.191 Angle : 0.790 12.814 4723 Z= 0.386 Chirality : 0.048 0.160 509 Planarity : 0.005 0.076 611 Dihedral : 5.338 25.605 504 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.03 % Allowed : 23.46 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.39), residues: 428 helix: -2.50 (0.91), residues: 28 sheet: -0.41 (0.44), residues: 134 loop : -1.06 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 498 TYR 0.017 0.002 TYR B 32 PHE 0.020 0.002 PHE B 83 TRP 0.009 0.001 TRP A 106 HIS 0.001 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 3462) covalent geometry : angle 0.78274 / 0.38 ( 4708) SS BOND : bond 0.00769 / 0.40 ( 6) SS BOND : angle 1.90586 / 0.98 ( 12) hydrogen bonds : bond 0.03747 / 2.56 ( 92) hydrogen bonds : angle 5.93091 / 4.00 ( 237) link_NAG-ASN : bond 0.00200 / 0.11 ( 1) link_NAG-ASN : angle 2.36350 / 1.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.7659 (m-80) cc_final: 0.7186 (m-80) REVERT: A 120 GLN cc_start: 0.8867 (mm110) cc_final: 0.8602 (mm-40) REVERT: C 392 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6517 (p90) REVERT: C 406 GLU cc_start: 0.8561 (pt0) cc_final: 0.8209 (pm20) REVERT: C 440 LYS cc_start: 0.8578 (tptp) cc_final: 0.8240 (tptp) REVERT: C 493 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7674 (mp10) REVERT: C 515 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8136 (p90) outliers start: 18 outliers final: 12 residues processed: 67 average time/residue: 0.3741 time to fit residues: 26.1418 Evaluate side-chains 69 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [35, 41, 13, 0, 2, 19, 10, 8, 33, 9, 30] chunk 35 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.094918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.083637 restraints weight = 11415.566| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 4.49 r_work: 0.3494 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3469 Z= 0.167 Angle : 0.793 13.238 4723 Z= 0.382 Chirality : 0.047 0.158 509 Planarity : 0.005 0.054 611 Dihedral : 5.187 24.681 504 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 5.03 % Allowed : 24.58 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.40), residues: 428 helix: -2.05 (1.09), residues: 22 sheet: -0.37 (0.45), residues: 134 loop : -1.05 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 498 TYR 0.010 0.001 TYR B 92 PHE 0.017 0.001 PHE B 83 TRP 0.008 0.001 TRP A 106 HIS 0.001 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 3462) covalent geometry : angle 0.78676 / 0.38 ( 4708) SS BOND : bond 0.00730 / 0.38 ( 6) SS BOND : angle 1.82051 / 0.94 ( 12) hydrogen bonds : bond 0.03691 / 2.51 ( 92) hydrogen bonds : angle 5.95199 / 3.99 ( 237) link_NAG-ASN : bond 0.00218 / 0.11 ( 1) link_NAG-ASN : angle 2.17659 / 1.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.7669 (m-80) cc_final: 0.7196 (m-80) REVERT: A 120 GLN cc_start: 0.8838 (mm110) cc_final: 0.8603 (mm-40) REVERT: B 42 LYS cc_start: 0.8943 (mmmm) cc_final: 0.8689 (mmmm) REVERT: C 392 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6513 (p90) REVERT: C 406 GLU cc_start: 0.8594 (pt0) cc_final: 0.8188 (pm20) REVERT: C 440 LYS cc_start: 0.8661 (tptp) cc_final: 0.8341 (tptp) REVERT: C 515 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8121 (p90) outliers start: 18 outliers final: 13 residues processed: 70 average time/residue: 0.3986 time to fit residues: 29.0147 Evaluate side-chains 71 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [23, 32, 34, 41, 10, 12, 16, 36, 14, 6, 40] chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.094190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.082899 restraints weight = 11509.096| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 4.49 r_work: 0.3478 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3469 Z= 0.190 Angle : 0.816 13.466 4723 Z= 0.397 Chirality : 0.048 0.203 509 Planarity : 0.005 0.063 611 Dihedral : 5.364 25.117 504 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.03 % Allowed : 25.14 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.39), residues: 428 helix: -2.47 (0.91), residues: 28 sheet: -0.36 (0.45), residues: 134 loop : -1.12 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 498 TYR 0.017 0.002 TYR B 49 PHE 0.015 0.002 PHE B 83 TRP 0.009 0.001 TRP A 106 HIS 0.001 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 ( 3462) covalent geometry : angle 0.80892 / 0.39 ( 4708) SS BOND : bond 0.00763 / 0.40 ( 6) SS BOND : angle 1.95136 / 1.01 ( 12) hydrogen bonds : bond 0.03775 / 2.58 ( 92) hydrogen bonds : angle 6.01666 / 4.04 ( 237) link_NAG-ASN : bond 0.00189 / 0.10 ( 1) link_NAG-ASN : angle 2.33195 / 1.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.7757 (m-80) cc_final: 0.7271 (m-80) REVERT: A 120 GLN cc_start: 0.8838 (mm110) cc_final: 0.8635 (mm-40) REVERT: B 42 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8711 (mmmm) REVERT: C 392 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6544 (p90) REVERT: C 406 GLU cc_start: 0.8572 (pt0) cc_final: 0.8165 (pm20) REVERT: C 440 LYS cc_start: 0.8598 (tptp) cc_final: 0.8257 (tptp) REVERT: C 493 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: C 515 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8150 (p90) outliers start: 18 outliers final: 12 residues processed: 70 average time/residue: 0.4059 time to fit residues: 29.4999 Evaluate side-chains 73 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [31, 7, 9, 3, 33, 19, 16, 10, 8, 36, 20] chunk 31 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.093139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.081945 restraints weight = 11544.677| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 4.50 r_work: 0.3462 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3469 Z= 0.229 Angle : 0.878 14.016 4723 Z= 0.429 Chirality : 0.050 0.224 509 Planarity : 0.006 0.081 611 Dihedral : 5.654 27.648 504 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.31 % Allowed : 25.42 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.39), residues: 428 helix: -1.89 (1.15), residues: 22 sheet: -0.35 (0.46), residues: 126 loop : -1.22 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 498 TYR 0.014 0.002 TYR B 92 PHE 0.015 0.002 PHE B 83 TRP 0.011 0.002 TRP A 106 HIS 0.001 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 ( 3462) covalent geometry : angle 0.87011 / 0.43 ( 4708) SS BOND : bond 0.00826 / 0.42 ( 6) SS BOND : angle 2.16574 / 1.12 ( 12) hydrogen bonds : bond 0.03996 / 2.73 ( 92) hydrogen bonds : angle 6.06125 / 4.07 ( 237) link_NAG-ASN : bond 0.00256 / 0.13 ( 1) link_NAG-ASN : angle 2.45290 / 1.34 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.7830 (m-80) cc_final: 0.7350 (m-80) REVERT: B 42 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8750 (mmmm) REVERT: C 392 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.7009 (p90) REVERT: C 406 GLU cc_start: 0.8587 (pt0) cc_final: 0.8172 (pm20) REVERT: C 440 LYS cc_start: 0.8579 (tptp) cc_final: 0.8252 (tptp) REVERT: C 493 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7715 (mp10) REVERT: C 515 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8126 (p90) outliers start: 19 outliers final: 12 residues processed: 72 average time/residue: 0.3960 time to fit residues: 29.6810 Evaluate side-chains 72 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: [38, 0, 15, 31, 3, 2, 40, 27, 8, 6, 39] chunk 38 optimal weight: 0.0070 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.096263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.084822 restraints weight = 11344.051| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 4.58 r_work: 0.3518 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3469 Z= 0.143 Angle : 0.845 13.716 4723 Z= 0.405 Chirality : 0.048 0.212 509 Planarity : 0.006 0.092 611 Dihedral : 5.202 30.189 504 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.19 % Allowed : 26.54 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.39), residues: 428 helix: -1.98 (1.17), residues: 20 sheet: 0.13 (0.48), residues: 116 loop : -1.22 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 498 TYR 0.020 0.001 TYR B 32 PHE 0.014 0.001 PHE B 83 TRP 0.008 0.001 TRP C 436 HIS 0.000 0.000 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 3462) covalent geometry : angle 0.84001 / 0.40 ( 4708) SS BOND : bond 0.00656 / 0.36 ( 6) SS BOND : angle 1.65900 / 0.85 ( 12) hydrogen bonds : bond 0.03654 / 2.51 ( 92) hydrogen bonds : angle 5.94090 / 3.97 ( 237) link_NAG-ASN : bond 0.00101 / 0.05 ( 1) link_NAG-ASN : angle 2.15872 / 1.21 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1323.90 seconds wall clock time: 23 minutes 27.43 seconds (1407.43 seconds total)