Starting phenix.real_space_refine on Fri Aug 22 13:40:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hed_34688/08_2025/8hed_34688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hed_34688/08_2025/8hed_34688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hed_34688/08_2025/8hed_34688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hed_34688/08_2025/8hed_34688.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hed_34688/08_2025/8hed_34688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hed_34688/08_2025/8hed_34688.map" } resolution = 3.59 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= -0.002 sd= 0.022 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 18 5.16 5 C 2102 2.51 5 N 547 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 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3318 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1578 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "G" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "O" 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 Chain: "B" 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: 1.09, per 1000 atoms: 0.33 Number of scatterers: 3318 At special positions: 0 Unit cell: (79.54, 62.32, 102.5, 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 18 16.00 O 651 8.00 N 547 7.00 C 2102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.04 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 92 " 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 O 1 " - " NAG O 2 " NAG-ASN " NAG B 601 " - " ASN B 331 " " NAG O 1 " - " ASN B 343 " Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 140.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 11.7% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.666A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.546A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.506A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.765A 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 78 through 82 removed outlier: 3.820A pdb=" N ASP F 81 " --> pdb=" O GLN F 78 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA F 82 " --> pdb=" O CYS F 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 78 through 82' Processing helix chain 'G' and resid 27 through 31 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.192A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.692A pdb=" N VAL F 18 " --> pdb=" O MET F 74 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS F 69 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR F 71 " --> pdb=" O SER F 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 9 through 13 removed outlier: 3.569A pdb=" N VAL F 108 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 12 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS F 110 " --> pdb=" O ALA F 12 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE F 47 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN F 36 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU F 45 " --> pdb=" O GLN F 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 9 through 13 removed outlier: 3.569A pdb=" N VAL F 108 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 12 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS F 110 " --> pdb=" O ALA F 12 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY F 89 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA F 100 " --> pdb=" O GLY F 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'G' and resid 10 through 11 removed outlier: 7.196A pdb=" N MET G 33 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE G 49 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.981A pdb=" N PHE G 106 " --> pdb=" O ARG G 94 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 252 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: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1054 1.35 - 1.47: 906 1.47 - 1.59: 1418 1.59 - 1.71: 0 1.71 - 1.83: 21 Bond restraints: 3399 Sorted by residual: bond pdb=" N ASN B 501 " pdb=" CA ASN B 501 " ideal model delta sigma weight residual 1.453 1.483 -0.030 1.22e-02 6.72e+03 6.06e+00 bond pdb=" N CYS F 98 " pdb=" CA CYS F 98 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.04e+00 bond pdb=" N GLU F 90 " pdb=" CA GLU F 90 " ideal model delta sigma weight residual 1.454 1.486 -0.033 1.34e-02 5.57e+03 5.97e+00 bond pdb=" N THR F 99 " pdb=" CA THR F 99 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.78e+00 bond pdb=" N CYS F 93 " pdb=" CA CYS F 93 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.47e+00 ... (remaining 3394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 4338 1.27 - 2.55: 222 2.55 - 3.82: 55 3.82 - 5.09: 7 5.09 - 6.37: 3 Bond angle restraints: 4625 Sorted by residual: angle pdb=" CA ASP F 97 " pdb=" C ASP F 97 " pdb=" O ASP F 97 " ideal model delta sigma weight residual 121.78 118.20 3.58 1.12e+00 7.97e-01 1.02e+01 angle pdb=" CA LYS G 63 " pdb=" CB LYS G 63 " pdb=" CG LYS G 63 " ideal model delta sigma weight residual 114.10 120.40 -6.30 2.00e+00 2.50e-01 9.91e+00 angle pdb=" CA GLU F 90 " pdb=" C GLU F 90 " pdb=" O GLU F 90 " ideal model delta sigma weight residual 121.87 118.35 3.52 1.16e+00 7.43e-01 9.22e+00 angle pdb=" CA ARG B 403 " pdb=" C ARG B 403 " pdb=" O ARG B 403 " ideal model delta sigma weight residual 121.87 118.71 3.16 1.10e+00 8.26e-01 8.23e+00 angle pdb=" CA PHE F 91 " pdb=" C PHE F 91 " pdb=" O PHE F 91 " ideal model delta sigma weight residual 122.31 118.61 3.70 1.31e+00 5.83e-01 7.98e+00 ... (remaining 4620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 1740 14.74 - 29.48: 203 29.48 - 44.21: 64 44.21 - 58.95: 12 58.95 - 73.69: 3 Dihedral angle restraints: 2022 sinusoidal: 802 harmonic: 1220 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -37.18 -48.82 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 54.96 38.04 1 1.00e+01 1.00e-02 2.04e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 58.20 34.80 1 1.00e+01 1.00e-02 1.72e+01 ... (remaining 2019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 302 0.029 - 0.058: 129 0.058 - 0.087: 39 0.087 - 0.116: 41 0.116 - 0.146: 7 Chirality restraints: 518 Sorted by residual: chirality pdb=" CA LEU G 28 " pdb=" N LEU G 28 " pdb=" C LEU G 28 " pdb=" CB LEU G 28 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA PHE F 91 " pdb=" N PHE F 91 " pdb=" C PHE F 91 " pdb=" CB PHE F 91 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA PRO B 337 " pdb=" N PRO B 337 " pdb=" C PRO B 337 " pdb=" CB PRO B 337 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 515 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 63 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C LYS G 63 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS G 63 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY G 64 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 468 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C ILE B 468 " 0.020 2.00e-02 2.50e+03 pdb=" O ILE B 468 " -0.007 2.00e-02 2.50e+03 pdb=" N SER B 469 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 89 " -0.005 2.00e-02 2.50e+03 1.03e-02 1.05e+00 pdb=" C GLY F 89 " 0.018 2.00e-02 2.50e+03 pdb=" O GLY F 89 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU F 90 " -0.006 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 698 2.78 - 3.31: 2933 3.31 - 3.84: 5034 3.84 - 4.37: 5680 4.37 - 4.90: 10270 Nonbonded interactions: 24615 Sorted by model distance: nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.247 3.040 nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.247 3.040 nonbonded pdb=" N GLU B 340 " pdb=" OE1 GLU B 340 " model vdw 2.254 3.120 nonbonded pdb=" OH TYR F 35 " pdb=" O VAL G 103 " model vdw 2.318 3.040 nonbonded pdb=" OD1 ASP G 52 " pdb=" N SER G 53 " model vdw 2.360 3.120 ... (remaining 24610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.760 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.090 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 0.033 3408 Z= 0.225 Angle : 0.680 6.368 4646 Z= 0.378 Chirality : 0.044 0.146 518 Planarity : 0.003 0.026 592 Dihedral : 13.888 73.689 1232 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.65 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 18.21 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.42), residues: 421 helix: -2.38 (1.25), residues: 15 sheet: 1.03 (0.49), residues: 136 loop : -0.94 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 30 TYR 0.007 0.001 TYR B 495 PHE 0.007 0.001 PHE B 342 TRP 0.005 0.001 TRP G 61 HIS 0.001 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3399) covalent geometry : angle 0.67002 ( 4625) SS BOND : bond 0.00441 ( 6) SS BOND : angle 1.84634 ( 12) hydrogen bonds : bond 0.26743 ( 94) hydrogen bonds : angle 9.66867 ( 252) link_BETA1-4 : bond 0.00631 ( 1) link_BETA1-4 : angle 0.86024 ( 3) link_NAG-ASN : bond 0.00512 ( 2) link_NAG-ASN : angle 2.07250 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.134 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1176 time to fit residues: 9.0956 Evaluate side-chains 63 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.0980 chunk 26 optimal weight: 0.0040 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.079696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.069737 restraints weight = 10120.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.072114 restraints weight = 4726.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.073736 restraints weight = 2796.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.074833 restraints weight = 1884.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.075606 restraints weight = 1390.451| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3408 Z= 0.117 Angle : 0.583 8.431 4646 Z= 0.301 Chirality : 0.043 0.150 518 Planarity : 0.003 0.022 592 Dihedral : 5.136 34.814 529 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.41 % Favored : 93.35 % Rotamer: Outliers : 3.36 % Allowed : 17.09 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.42), residues: 421 helix: -1.88 (1.40), residues: 15 sheet: 1.15 (0.46), residues: 148 loop : -1.06 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 30 TYR 0.010 0.001 TYR B 453 PHE 0.008 0.001 PHE B 342 TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3399) covalent geometry : angle 0.57970 ( 4625) SS BOND : bond 0.00527 ( 6) SS BOND : angle 1.08164 ( 12) hydrogen bonds : bond 0.04629 ( 94) hydrogen bonds : angle 6.89969 ( 252) link_BETA1-4 : bond 0.00550 ( 1) link_BETA1-4 : angle 0.88930 ( 3) link_NAG-ASN : bond 0.00529 ( 2) link_NAG-ASN : angle 1.33432 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.4156 (t0) cc_final: 0.3936 (t0) REVERT: G 52 ASP cc_start: 0.8885 (p0) cc_final: 0.8660 (p0) outliers start: 12 outliers final: 7 residues processed: 78 average time/residue: 0.0913 time to fit residues: 8.3404 Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.075247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.065596 restraints weight = 10182.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.067870 restraints weight = 4708.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.069385 restraints weight = 2769.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070413 restraints weight = 1861.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071154 restraints weight = 1375.442| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 3408 Z= 0.277 Angle : 0.673 5.085 4646 Z= 0.355 Chirality : 0.047 0.153 518 Planarity : 0.004 0.030 592 Dihedral : 6.150 38.616 529 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.55 % Favored : 91.21 % Rotamer: Outliers : 3.92 % Allowed : 19.89 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.42), residues: 421 helix: -1.40 (1.51), residues: 15 sheet: 1.10 (0.47), residues: 139 loop : -1.32 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 454 TYR 0.015 0.002 TYR B 495 PHE 0.012 0.002 PHE G 91 TRP 0.008 0.001 TRP G 46 HIS 0.003 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 3399) covalent geometry : angle 0.66283 ( 4625) SS BOND : bond 0.00709 ( 6) SS BOND : angle 1.98415 ( 12) hydrogen bonds : bond 0.04921 ( 94) hydrogen bonds : angle 6.54446 ( 252) link_BETA1-4 : bond 0.00682 ( 1) link_BETA1-4 : angle 1.34453 ( 3) link_NAG-ASN : bond 0.00924 ( 2) link_NAG-ASN : angle 1.78815 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: F 23 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7923 (tm-30) REVERT: F 35 TYR cc_start: 0.9274 (m-80) cc_final: 0.8995 (m-80) REVERT: F 97 ASP cc_start: 0.8789 (m-30) cc_final: 0.8485 (m-30) outliers start: 14 outliers final: 10 residues processed: 74 average time/residue: 0.0779 time to fit residues: 6.7958 Evaluate side-chains 76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 112 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.0020 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.078134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.068441 restraints weight = 10110.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.070805 restraints weight = 4682.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.072392 restraints weight = 2753.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.073462 restraints weight = 1849.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.074227 restraints weight = 1366.204| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3408 Z= 0.132 Angle : 0.591 8.136 4646 Z= 0.305 Chirality : 0.044 0.158 518 Planarity : 0.004 0.046 592 Dihedral : 5.494 34.209 529 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.89 % Favored : 92.87 % Rotamer: Outliers : 3.64 % Allowed : 20.73 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.42), residues: 421 helix: -1.47 (1.54), residues: 15 sheet: 1.17 (0.45), residues: 147 loop : -1.27 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.010 0.001 TYR B 453 PHE 0.008 0.001 PHE B 342 TRP 0.006 0.001 TRP G 46 HIS 0.001 0.000 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3399) covalent geometry : angle 0.58129 ( 4625) SS BOND : bond 0.00666 ( 6) SS BOND : angle 1.70951 ( 12) hydrogen bonds : bond 0.03850 ( 94) hydrogen bonds : angle 6.14311 ( 252) link_BETA1-4 : bond 0.00660 ( 1) link_BETA1-4 : angle 1.27167 ( 3) link_NAG-ASN : bond 0.00545 ( 2) link_NAG-ASN : angle 1.80632 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.079 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 79 average time/residue: 0.0803 time to fit residues: 7.4667 Evaluate side-chains 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.076930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.067430 restraints weight = 10063.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.069702 restraints weight = 4575.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.071207 restraints weight = 2661.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.072248 restraints weight = 1778.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.072949 restraints weight = 1302.450| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3408 Z= 0.140 Angle : 0.604 8.036 4646 Z= 0.309 Chirality : 0.044 0.157 518 Planarity : 0.003 0.032 592 Dihedral : 5.390 33.703 529 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.08 % Favored : 91.69 % Rotamer: Outliers : 4.48 % Allowed : 20.17 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.42), residues: 421 helix: -1.47 (1.50), residues: 15 sheet: 1.23 (0.46), residues: 146 loop : -1.29 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.011 0.001 TYR B 453 PHE 0.009 0.001 PHE B 486 TRP 0.007 0.001 TRP G 46 HIS 0.001 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3399) covalent geometry : angle 0.58940 ( 4625) SS BOND : bond 0.00877 ( 6) SS BOND : angle 2.29547 ( 12) hydrogen bonds : bond 0.03702 ( 94) hydrogen bonds : angle 5.92152 ( 252) link_BETA1-4 : bond 0.00788 ( 1) link_BETA1-4 : angle 1.21714 ( 3) link_NAG-ASN : bond 0.00557 ( 2) link_NAG-ASN : angle 1.79902 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.4626 (t0) cc_final: 0.4326 (t0) REVERT: F 23 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7799 (tm-30) outliers start: 16 outliers final: 11 residues processed: 77 average time/residue: 0.0894 time to fit residues: 8.0428 Evaluate side-chains 76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 112 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.075918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.066598 restraints weight = 9961.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068823 restraints weight = 4496.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.070266 restraints weight = 2599.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.071268 restraints weight = 1739.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.071981 restraints weight = 1273.125| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3408 Z= 0.178 Angle : 0.630 6.851 4646 Z= 0.324 Chirality : 0.044 0.157 518 Planarity : 0.004 0.030 592 Dihedral : 5.539 34.542 529 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.55 % Favored : 91.21 % Rotamer: Outliers : 4.20 % Allowed : 19.89 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.42), residues: 421 helix: -1.49 (1.49), residues: 15 sheet: 1.10 (0.46), residues: 147 loop : -1.43 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 65 TYR 0.012 0.001 TYR B 453 PHE 0.010 0.001 PHE B 342 TRP 0.007 0.001 TRP G 46 HIS 0.002 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 3399) covalent geometry : angle 0.61862 ( 4625) SS BOND : bond 0.00833 ( 6) SS BOND : angle 2.01571 ( 12) hydrogen bonds : bond 0.03745 ( 94) hydrogen bonds : angle 5.90594 ( 252) link_BETA1-4 : bond 0.00518 ( 1) link_BETA1-4 : angle 1.19661 ( 3) link_NAG-ASN : bond 0.00645 ( 2) link_NAG-ASN : angle 1.88442 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: F 23 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7794 (tm-30) REVERT: F 75 ARG cc_start: 0.7876 (ttm110) cc_final: 0.7522 (mtm-85) REVERT: F 97 ASP cc_start: 0.8748 (m-30) cc_final: 0.8519 (m-30) outliers start: 15 outliers final: 11 residues processed: 75 average time/residue: 0.0777 time to fit residues: 6.8886 Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 112 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.076436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.066893 restraints weight = 10245.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.069143 restraints weight = 4614.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.070669 restraints weight = 2673.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.071693 restraints weight = 1772.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.072421 restraints weight = 1297.140| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3408 Z= 0.153 Angle : 0.625 6.952 4646 Z= 0.316 Chirality : 0.043 0.158 518 Planarity : 0.003 0.032 592 Dihedral : 5.347 33.664 529 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.20 % Allowed : 21.01 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.42), residues: 421 helix: -1.58 (1.46), residues: 15 sheet: 1.03 (0.47), residues: 141 loop : -1.30 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 30 TYR 0.009 0.001 TYR B 453 PHE 0.009 0.001 PHE B 342 TRP 0.006 0.001 TRP G 46 HIS 0.002 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 3399) covalent geometry : angle 0.61548 ( 4625) SS BOND : bond 0.00754 ( 6) SS BOND : angle 1.75335 ( 12) hydrogen bonds : bond 0.03546 ( 94) hydrogen bonds : angle 5.77235 ( 252) link_BETA1-4 : bond 0.00701 ( 1) link_BETA1-4 : angle 1.26430 ( 3) link_NAG-ASN : bond 0.00602 ( 2) link_NAG-ASN : angle 1.92906 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.4279 (t0) cc_final: 0.3793 (t0) REVERT: F 23 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7798 (tm-30) REVERT: F 35 TYR cc_start: 0.9208 (m-80) cc_final: 0.8947 (m-80) REVERT: F 97 ASP cc_start: 0.8754 (m-30) cc_final: 0.8536 (m-30) outliers start: 15 outliers final: 13 residues processed: 77 average time/residue: 0.0809 time to fit residues: 7.3869 Evaluate side-chains 80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 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 = 0.3302 r_free = 0.3302 target = 0.076556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.067081 restraints weight = 10204.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069337 restraints weight = 4578.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.070858 restraints weight = 2627.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.071866 restraints weight = 1735.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.072581 restraints weight = 1271.023| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3408 Z= 0.148 Angle : 0.625 8.713 4646 Z= 0.315 Chirality : 0.043 0.156 518 Planarity : 0.003 0.033 592 Dihedral : 5.277 33.228 529 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.92 % Allowed : 20.73 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.42), residues: 421 helix: -1.64 (1.43), residues: 15 sheet: 1.03 (0.47), residues: 141 loop : -1.29 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.010 0.001 TYR B 453 PHE 0.009 0.001 PHE B 342 TRP 0.006 0.001 TRP G 46 HIS 0.002 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3399) covalent geometry : angle 0.61605 ( 4625) SS BOND : bond 0.00713 ( 6) SS BOND : angle 1.58166 ( 12) hydrogen bonds : bond 0.03476 ( 94) hydrogen bonds : angle 5.69240 ( 252) link_BETA1-4 : bond 0.00721 ( 1) link_BETA1-4 : angle 1.25529 ( 3) link_NAG-ASN : bond 0.00574 ( 2) link_NAG-ASN : angle 1.94378 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.4182 (t0) cc_final: 0.3718 (t0) REVERT: F 62 ARG cc_start: 0.8038 (tmm-80) cc_final: 0.7639 (mtp180) REVERT: F 97 ASP cc_start: 0.8748 (m-30) cc_final: 0.8532 (m-30) outliers start: 14 outliers final: 12 residues processed: 77 average time/residue: 0.0847 time to fit residues: 7.7657 Evaluate side-chains 78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.0020 chunk 4 optimal weight: 0.7980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.077399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.067933 restraints weight = 9980.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.070219 restraints weight = 4512.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.071732 restraints weight = 2597.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.072773 restraints weight = 1720.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.073450 restraints weight = 1253.133| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3408 Z= 0.129 Angle : 0.641 9.216 4646 Z= 0.317 Chirality : 0.043 0.156 518 Planarity : 0.003 0.031 592 Dihedral : 5.072 31.488 529 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.36 % Allowed : 21.29 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.42), residues: 421 helix: -2.65 (1.07), residues: 21 sheet: 0.97 (0.47), residues: 141 loop : -1.17 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.009 0.001 TYR B 453 PHE 0.008 0.001 PHE B 342 TRP 0.006 0.001 TRP G 61 HIS 0.001 0.000 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3399) covalent geometry : angle 0.63364 ( 4625) SS BOND : bond 0.00663 ( 6) SS BOND : angle 1.43255 ( 12) hydrogen bonds : bond 0.03400 ( 94) hydrogen bonds : angle 5.59179 ( 252) link_BETA1-4 : bond 0.00713 ( 1) link_BETA1-4 : angle 1.17919 ( 3) link_NAG-ASN : bond 0.00481 ( 2) link_NAG-ASN : angle 1.91765 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.4112 (t0) cc_final: 0.3681 (t0) REVERT: F 23 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7797 (tm-30) REVERT: F 62 ARG cc_start: 0.8042 (tmm-80) cc_final: 0.7597 (mtp-110) REVERT: F 97 ASP cc_start: 0.8740 (m-30) cc_final: 0.8521 (m-30) outliers start: 12 outliers final: 12 residues processed: 77 average time/residue: 0.0855 time to fit residues: 7.7438 Evaluate side-chains 80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.078239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069174 restraints weight = 10037.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.071435 restraints weight = 4481.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.072919 restraints weight = 2561.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.073906 restraints weight = 1692.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.074559 restraints weight = 1232.768| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3408 Z= 0.166 Angle : 0.655 8.519 4646 Z= 0.327 Chirality : 0.044 0.156 518 Planarity : 0.003 0.034 592 Dihedral : 5.293 32.977 529 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.64 % Allowed : 21.29 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.42), residues: 421 helix: -2.65 (1.07), residues: 21 sheet: 0.72 (0.46), residues: 147 loop : -1.12 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.011 0.001 TYR B 453 PHE 0.010 0.001 PHE G 91 TRP 0.005 0.001 TRP G 46 HIS 0.002 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3399) covalent geometry : angle 0.64687 ( 4625) SS BOND : bond 0.00688 ( 6) SS BOND : angle 1.50959 ( 12) hydrogen bonds : bond 0.03589 ( 94) hydrogen bonds : angle 5.68214 ( 252) link_BETA1-4 : bond 0.00729 ( 1) link_BETA1-4 : angle 1.25922 ( 3) link_NAG-ASN : bond 0.00639 ( 2) link_NAG-ASN : angle 2.01162 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: F 23 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7879 (tm-30) REVERT: F 62 ARG cc_start: 0.8011 (tmm-80) cc_final: 0.7777 (mtp180) outliers start: 13 outliers final: 13 residues processed: 77 average time/residue: 0.0756 time to fit residues: 6.9157 Evaluate side-chains 81 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 29 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.079151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.069882 restraints weight = 9910.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.072134 restraints weight = 4445.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.073624 restraints weight = 2560.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.074631 restraints weight = 1707.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075289 restraints weight = 1249.031| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3408 Z= 0.139 Angle : 0.680 9.108 4646 Z= 0.339 Chirality : 0.044 0.157 518 Planarity : 0.004 0.037 592 Dihedral : 5.240 31.897 529 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.64 % Allowed : 21.85 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.42), residues: 421 helix: -2.69 (1.06), residues: 21 sheet: 0.85 (0.47), residues: 141 loop : -1.20 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.010 0.001 TYR B 453 PHE 0.008 0.001 PHE G 91 TRP 0.006 0.001 TRP B 436 HIS 0.001 0.001 HIS G 55 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 3399) covalent geometry : angle 0.66599 ( 4625) SS BOND : bond 0.00629 ( 6) SS BOND : angle 2.35568 ( 12) hydrogen bonds : bond 0.03475 ( 94) hydrogen bonds : angle 5.66662 ( 252) link_BETA1-4 : bond 0.00704 ( 1) link_BETA1-4 : angle 1.25577 ( 3) link_NAG-ASN : bond 0.00534 ( 2) link_NAG-ASN : angle 1.99430 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 968.35 seconds wall clock time: 17 minutes 17.34 seconds (1037.34 seconds total)