Starting phenix.real_space_refine on Wed Jul 1 21:49:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bg6_16024/07_2026/8bg6_16024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bg6_16024/07_2026/8bg6_16024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8bg6_16024/07_2026/8bg6_16024.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bg6_16024/07_2026/8bg6_16024.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bg6_16024/07_2026/8bg6_16024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bg6_16024/07_2026/8bg6_16024.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bg6_16024/07_2026/8bg6_16024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bg6_16024/07_2026/8bg6_16024.map" } resolution = 4.11 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.017 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 16 5.16 5 C 1981 2.51 5 N 527 2.21 5 O 600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3124 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 845 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1450 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 172} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" 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 chiralities: 1 Time building chain proxies: 0.72, per 1000 atoms: 0.23 Number of scatterers: 3124 At special positions: 0 Unit cell: (66.64, 65.96, 94.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 600 8.00 N 527 7.00 C 1981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=1.94 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 NAG-ASN " NAG E2000 " - " ASN E 343 " Time building additional restraints: 0.14 Conformation dependent library (CDL) restraints added in 73.4 milliseconds 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 728 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 8.3% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.596A pdb=" N THR A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 342 removed outlier: 3.781A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.681A pdb=" N ALA E 352 " --> pdb=" O SER E 349 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 349 through 353' Processing helix chain 'E' and resid 384 through 388 removed outlier: 3.579A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 384 through 388' Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.683A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.583A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.072A pdb=" N GLY A 10 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 37 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.524A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR B 49 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS B 53 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 24 Processing sheet with id=AA5, first strand: chain 'E' and resid 355 through 358 removed outlier: 7.161A pdb=" N ASN E 437 " --> pdb=" O PHE E 374 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE E 374 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.500A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 198 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: 0.25 Time building geometry restraints manager: 0.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 757 1.33 - 1.45: 729 1.45 - 1.57: 1696 1.57 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 3202 Sorted by residual: bond pdb=" N SER A 31 " pdb=" CA SER A 31 " ideal model delta sigma weight residual 1.458 1.485 -0.026 9.00e-03 1.23e+04 8.67e+00 bond pdb=" N ASN E 343 " pdb=" CA ASN E 343 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.06e-02 8.90e+03 8.49e+00 bond pdb=" N GLU A 26 " pdb=" CA GLU A 26 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.41e+00 bond pdb=" N VAL E 362 " pdb=" CA VAL E 362 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.19e-02 7.06e+03 8.09e+00 bond pdb=" N TYR A 93 " pdb=" CA TYR A 93 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.16e-02 7.43e+03 7.95e+00 ... (remaining 3197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 4044 1.73 - 3.46: 254 3.46 - 5.19: 44 5.19 - 6.93: 7 6.93 - 8.66: 3 Bond angle restraints: 4352 Sorted by residual: angle pdb=" CB LYS E 386 " pdb=" CG LYS E 386 " pdb=" CD LYS E 386 " ideal model delta sigma weight residual 111.30 119.96 -8.66 2.30e+00 1.89e-01 1.42e+01 angle pdb=" CA THR A 108 " pdb=" C THR A 108 " pdb=" O THR A 108 " ideal model delta sigma weight residual 121.46 117.15 4.31 1.17e+00 7.31e-01 1.36e+01 angle pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" O ILE A 103 " ideal model delta sigma weight residual 120.25 116.69 3.56 9.90e-01 1.02e+00 1.29e+01 angle pdb=" C ILE A 103 " pdb=" N TRP A 104 " pdb=" CA TRP A 104 " ideal model delta sigma weight residual 123.00 127.93 -4.93 1.38e+00 5.25e-01 1.28e+01 angle pdb=" CA GLN E 474 " pdb=" CB GLN E 474 " pdb=" CG GLN E 474 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.21e+01 ... (remaining 4347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 1687 15.98 - 31.95: 142 31.95 - 47.93: 39 47.93 - 63.91: 5 63.91 - 79.88: 2 Dihedral angle restraints: 1875 sinusoidal: 725 harmonic: 1150 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CA GLY A 105 " pdb=" C GLY A 105 " pdb=" N GLN A 106 " pdb=" CA GLN A 106 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" C SER A 31 " pdb=" N SER A 31 " pdb=" CA SER A 31 " pdb=" CB SER A 31 " ideal model delta harmonic sigma weight residual -122.60 -131.69 9.09 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 1872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 377 0.068 - 0.136: 75 0.136 - 0.204: 15 0.204 - 0.272: 0 0.272 - 0.340: 2 Chirality restraints: 469 Sorted by residual: chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA SER A 31 " pdb=" N SER A 31 " pdb=" C SER A 31 " pdb=" CB SER A 31 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA ASN A 76 " pdb=" N ASN A 76 " pdb=" C ASN A 76 " pdb=" CB ASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 466 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 40 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO A 41 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 96 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C ALA A 96 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA A 96 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 97 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 16 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C GLY A 16 " 0.033 2.00e-02 2.50e+03 pdb=" O GLY A 16 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 17 " -0.011 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1161 2.86 - 3.37: 2456 3.37 - 3.88: 4514 3.88 - 4.39: 4882 4.39 - 4.90: 8948 Nonbonded interactions: 21961 Sorted by model distance: nonbonded pdb=" O ASP B 28 " pdb=" OD1 ASP B 28 " model vdw 2.348 3.040 nonbonded pdb=" O MET A 99 " pdb=" CG ARG A 100 " model vdw 2.425 3.440 nonbonded pdb=" OE1 GLU A 102 " pdb=" OH TYR B 36 " model vdw 2.463 3.040 nonbonded pdb=" OD1 ASN E 448 " pdb=" N ASN E 450 " model vdw 2.473 3.120 nonbonded pdb=" O SER E 366 " pdb=" N TYR E 369 " model vdw 2.496 3.120 ... (remaining 21956 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: 1.480 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.180 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 : 0.006 0.088 3207 Z= 0.418 Angle : 0.953 9.554 4363 Z= 0.608 Chirality : 0.060 0.340 469 Planarity : 0.005 0.068 565 Dihedral : 12.642 79.885 1135 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % 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 are not related in a simple way. whole: -0.90 (0.43), residues: 392 helix: -3.56 (0.97), residues: 18 sheet: 0.73 (0.50), residues: 116 loop : -1.06 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 61 TYR 0.014 0.001 TYR E 473 PHE 0.011 0.001 PHE E 400 TRP 0.009 0.001 TRP E 436 HIS 0.006 0.002 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.41 ( 3202) covalent geometry : angle 0.93687 / 0.60 ( 4352) SS BOND : bond 0.04397 / 2.09 ( 4) SS BOND : angle 3.69740 / 1.93 ( 8) hydrogen bonds : bond 0.22035 / 15.58 ( 85) hydrogen bonds : angle 6.05639 / 4.16 ( 198) link_NAG-ASN : bond 0.04698 / 2.47 ( 1) link_NAG-ASN : angle 3.35730 / 1.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0694 time to fit residues: 6.8082 Evaluate side-chains 61 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 0.0970 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.0470 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS B 34 ASN ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.147394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.119371 restraints weight = 4384.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.118374 restraints weight = 5910.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.119166 restraints weight = 5417.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.119265 restraints weight = 4414.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.119278 restraints weight = 4132.866| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3207 Z= 0.104 Angle : 0.548 5.159 4363 Z= 0.290 Chirality : 0.045 0.135 469 Planarity : 0.004 0.034 565 Dihedral : 3.993 13.960 440 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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 are not related in a simple way. whole: -0.33 (0.44), residues: 392 helix: -3.41 (0.95), residues: 18 sheet: 0.62 (0.51), residues: 123 loop : -0.37 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 509 TYR 0.013 0.001 TYR E 453 PHE 0.009 0.001 PHE E 490 TRP 0.011 0.001 TRP E 436 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 3202) covalent geometry : angle 0.54588 / 0.29 ( 4352) SS BOND : bond 0.00495 / 0.24 ( 4) SS BOND : angle 1.06212 / 0.54 ( 8) hydrogen bonds : bond 0.03714 / 2.52 ( 85) hydrogen bonds : angle 5.04529 / 3.39 ( 198) link_NAG-ASN : bond 0.00270 / 0.14 ( 1) link_NAG-ASN : angle 0.81537 / 0.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8260 (t0) cc_final: 0.8040 (t0) REVERT: A 88 GLU cc_start: 0.7329 (tp30) cc_final: 0.6995 (tp30) REVERT: E 370 ASN cc_start: 0.8143 (p0) cc_final: 0.7939 (p0) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0724 time to fit residues: 7.2064 Evaluate side-chains 63 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 506 GLN ** 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 = 0.3600 r_free = 0.3600 target = 0.148415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.138681 restraints weight = 4348.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.131280 restraints weight = 6537.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.124722 restraints weight = 7061.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.126459 restraints weight = 6939.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.125943 restraints weight = 6282.902| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3207 Z= 0.114 Angle : 0.542 4.938 4363 Z= 0.289 Chirality : 0.044 0.131 469 Planarity : 0.004 0.035 565 Dihedral : 3.924 13.673 440 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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 are not related in a simple way. whole: -0.12 (0.44), residues: 392 helix: -3.31 (0.98), residues: 18 sheet: 0.67 (0.50), residues: 128 loop : -0.18 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 100 TYR 0.011 0.001 TYR B 36 PHE 0.011 0.001 PHE B 73 TRP 0.024 0.002 TRP A 36 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 3202) covalent geometry : angle 0.54032 / 0.29 ( 4352) SS BOND : bond 0.00549 / 0.26 ( 4) SS BOND : angle 1.03681 / 0.56 ( 8) hydrogen bonds : bond 0.03984 / 2.69 ( 85) hydrogen bonds : angle 4.95006 / 3.31 ( 198) link_NAG-ASN : bond 0.00171 / 0.09 ( 1) link_NAG-ASN : angle 0.91476 / 0.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.122 Fit side-chains REVERT: A 72 ASP cc_start: 0.8343 (t0) cc_final: 0.8017 (t0) REVERT: A 88 GLU cc_start: 0.7377 (tp30) cc_final: 0.7164 (tp30) REVERT: E 370 ASN cc_start: 0.7951 (p0) cc_final: 0.7666 (p0) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0645 time to fit residues: 6.2933 Evaluate side-chains 71 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 6.9990 chunk 36 optimal weight: 0.0060 chunk 35 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.138907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.128646 restraints weight = 4472.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.122245 restraints weight = 7893.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.116534 restraints weight = 7332.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.117874 restraints weight = 8383.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.118316 restraints weight = 5554.249| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3207 Z= 0.247 Angle : 0.668 5.758 4363 Z= 0.362 Chirality : 0.048 0.178 469 Planarity : 0.005 0.035 565 Dihedral : 4.582 16.208 440 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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 are not related in a simple way. whole: -0.42 (0.43), residues: 392 helix: -3.02 (0.80), residues: 30 sheet: 0.67 (0.49), residues: 128 loop : -0.41 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 19 TYR 0.017 0.002 TYR B 49 PHE 0.011 0.002 PHE B 73 TRP 0.038 0.003 TRP A 36 HIS 0.003 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 ( 3202) covalent geometry : angle 0.66486 / 0.36 ( 4352) SS BOND : bond 0.01182 / 0.57 ( 4) SS BOND : angle 1.58853 / 0.82 ( 8) hydrogen bonds : bond 0.05126 / 3.50 ( 85) hydrogen bonds : angle 5.66052 / 3.77 ( 198) link_NAG-ASN : bond 0.00032 / 0.02 ( 1) link_NAG-ASN : angle 1.29947 / 0.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: A 36 TRP cc_start: 0.8944 (t-100) cc_final: 0.8566 (m100) REVERT: B 79 GLN cc_start: 0.8771 (mp10) cc_final: 0.8528 (mp10) REVERT: E 370 ASN cc_start: 0.7868 (p0) cc_final: 0.7583 (p0) REVERT: E 465 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7505 (tp30) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0733 time to fit residues: 7.0752 Evaluate side-chains 69 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 506 GLN ** 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 = 0.3559 r_free = 0.3559 target = 0.144692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133507 restraints weight = 4318.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.132761 restraints weight = 8924.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.131025 restraints weight = 7680.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.130232 restraints weight = 6462.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.130377 restraints weight = 5682.609| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3207 Z= 0.104 Angle : 0.533 4.575 4363 Z= 0.285 Chirality : 0.044 0.131 469 Planarity : 0.004 0.045 565 Dihedral : 4.061 14.061 440 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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 are not related in a simple way. whole: -0.16 (0.44), residues: 392 helix: -3.17 (0.90), residues: 24 sheet: 0.63 (0.49), residues: 128 loop : -0.11 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 357 TYR 0.008 0.001 TYR E 453 PHE 0.011 0.001 PHE B 73 TRP 0.011 0.001 TRP E 436 HIS 0.005 0.002 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 3202) covalent geometry : angle 0.53193 / 0.28 ( 4352) SS BOND : bond 0.00523 / 0.25 ( 4) SS BOND : angle 0.78803 / 0.45 ( 8) hydrogen bonds : bond 0.03615 / 2.48 ( 85) hydrogen bonds : angle 5.07007 / 3.45 ( 198) link_NAG-ASN : bond 0.00162 / 0.09 ( 1) link_NAG-ASN : angle 0.82292 / 0.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.9198 (m) cc_final: 0.8605 (t) REVERT: A 36 TRP cc_start: 0.8888 (t-100) cc_final: 0.8167 (m100) REVERT: A 106 GLN cc_start: 0.8089 (tp40) cc_final: 0.7622 (mm-40) REVERT: B 79 GLN cc_start: 0.8809 (mp10) cc_final: 0.8592 (mp10) REVERT: B 91 CYS cc_start: 0.8754 (t) cc_final: 0.8372 (p) REVERT: E 370 ASN cc_start: 0.7096 (p0) cc_final: 0.6862 (p0) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0713 time to fit residues: 6.8963 Evaluate side-chains 70 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 6 optimal weight: 0.0970 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 31 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.146326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.135225 restraints weight = 4360.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.129074 restraints weight = 7975.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.123029 restraints weight = 6040.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.124018 restraints weight = 7976.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.124487 restraints weight = 5492.809| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3207 Z= 0.101 Angle : 0.529 4.516 4363 Z= 0.281 Chirality : 0.044 0.131 469 Planarity : 0.004 0.044 565 Dihedral : 3.966 13.332 440 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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 are not related in a simple way. whole: 0.02 (0.44), residues: 392 helix: -3.16 (0.88), residues: 24 sheet: 0.64 (0.46), residues: 141 loop : 0.06 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.010 0.001 TYR B 36 PHE 0.019 0.001 PHE A 67 TRP 0.011 0.001 TRP E 436 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 3202) covalent geometry : angle 0.52818 / 0.28 ( 4352) SS BOND : bond 0.00453 / 0.22 ( 4) SS BOND : angle 0.69598 / 0.43 ( 8) hydrogen bonds : bond 0.03539 / 2.46 ( 85) hydrogen bonds : angle 4.95164 / 3.40 ( 198) link_NAG-ASN : bond 0.00160 / 0.08 ( 1) link_NAG-ASN : angle 0.82678 / 0.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.9180 (m) cc_final: 0.8640 (t) REVERT: A 104 TRP cc_start: 0.8754 (m100) cc_final: 0.8401 (m100) REVERT: A 106 GLN cc_start: 0.8193 (tp40) cc_final: 0.7756 (mm-40) REVERT: E 370 ASN cc_start: 0.7780 (p0) cc_final: 0.7495 (p0) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0754 time to fit residues: 7.2697 Evaluate side-chains 70 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 18 optimal weight: 0.0670 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.136959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.125349 restraints weight = 4553.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.118783 restraints weight = 8774.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.112381 restraints weight = 8375.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.113785 restraints weight = 9829.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.114414 restraints weight = 6855.518| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 3207 Z= 0.304 Angle : 0.726 6.037 4363 Z= 0.393 Chirality : 0.050 0.198 469 Planarity : 0.005 0.041 565 Dihedral : 4.779 16.783 440 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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 are not related in a simple way. whole: -0.56 (0.43), residues: 392 helix: -3.12 (0.77), residues: 30 sheet: 0.34 (0.45), residues: 147 loop : -0.38 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 457 TYR 0.017 0.002 TYR B 49 PHE 0.014 0.002 PHE E 347 TRP 0.013 0.003 TRP A 47 HIS 0.008 0.002 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00714 / 0.30 ( 3202) covalent geometry : angle 0.72316 / 0.39 ( 4352) SS BOND : bond 0.01080 / 0.52 ( 4) SS BOND : angle 1.51701 / 0.78 ( 8) hydrogen bonds : bond 0.05680 / 3.86 ( 85) hydrogen bonds : angle 5.54918 / 3.62 ( 198) link_NAG-ASN : bond 0.00131 / 0.07 ( 1) link_NAG-ASN : angle 1.36477 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8037 (mmm) cc_final: 0.7680 (mpp) REVERT: A 106 GLN cc_start: 0.8327 (tp40) cc_final: 0.7941 (mm-40) REVERT: E 370 ASN cc_start: 0.7990 (p0) cc_final: 0.7678 (p0) REVERT: E 465 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7604 (tp30) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0557 time to fit residues: 5.2274 Evaluate side-chains 61 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 0.0000 chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.143650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.131000 restraints weight = 4531.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.131143 restraints weight = 8570.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.130778 restraints weight = 6770.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.130430 restraints weight = 5473.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.130681 restraints weight = 4700.433| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3207 Z= 0.113 Angle : 0.576 5.227 4363 Z= 0.304 Chirality : 0.045 0.131 469 Planarity : 0.004 0.046 565 Dihedral : 4.207 13.873 440 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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 are not related in a simple way. whole: -0.24 (0.44), residues: 392 helix: -3.22 (0.88), residues: 24 sheet: 0.38 (0.45), residues: 153 loop : -0.09 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 61 TYR 0.008 0.001 TYR E 453 PHE 0.015 0.001 PHE A 67 TRP 0.011 0.001 TRP E 436 HIS 0.004 0.002 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 3202) covalent geometry : angle 0.57505 / 0.30 ( 4352) SS BOND : bond 0.00518 / 0.25 ( 4) SS BOND : angle 0.80798 / 0.48 ( 8) hydrogen bonds : bond 0.03662 / 2.53 ( 85) hydrogen bonds : angle 5.10998 / 3.41 ( 198) link_NAG-ASN : bond 0.00150 / 0.08 ( 1) link_NAG-ASN : angle 0.79974 / 0.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8225 (tp40) cc_final: 0.7782 (mm-40) REVERT: E 370 ASN cc_start: 0.6971 (p0) cc_final: 0.6749 (p0) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0818 time to fit residues: 6.9625 Evaluate side-chains 65 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.136818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.122755 restraints weight = 4402.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.122502 restraints weight = 8370.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.119166 restraints weight = 5966.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.118740 restraints weight = 8154.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.118449 restraints weight = 7247.434| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3207 Z= 0.134 Angle : 0.599 4.548 4363 Z= 0.317 Chirality : 0.045 0.139 469 Planarity : 0.004 0.046 565 Dihedral : 4.184 13.285 440 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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 are not related in a simple way. whole: -0.27 (0.44), residues: 392 helix: -3.28 (0.87), residues: 24 sheet: 0.36 (0.44), residues: 155 loop : -0.11 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 61 TYR 0.010 0.001 TYR B 36 PHE 0.013 0.001 PHE A 67 TRP 0.011 0.001 TRP E 436 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 3202) covalent geometry : angle 0.59838 / 0.32 ( 4352) SS BOND : bond 0.00640 / 0.31 ( 4) SS BOND : angle 0.90590 / 0.51 ( 8) hydrogen bonds : bond 0.03840 / 2.66 ( 85) hydrogen bonds : angle 5.00243 / 3.32 ( 198) link_NAG-ASN : bond 0.00067 / 0.04 ( 1) link_NAG-ASN : angle 0.95529 / 0.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8293 (tp40) cc_final: 0.7879 (mm-40) REVERT: E 370 ASN cc_start: 0.7277 (p0) cc_final: 0.7030 (p0) REVERT: E 506 GLN cc_start: 0.8930 (mp-120) cc_final: 0.8501 (mp10) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0743 time to fit residues: 6.3741 Evaluate side-chains 63 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.138438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.125930 restraints weight = 4324.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.124929 restraints weight = 7965.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.123889 restraints weight = 7149.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.123423 restraints weight = 5731.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.123571 restraints weight = 5080.319| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3207 Z= 0.117 Angle : 0.589 6.212 4363 Z= 0.311 Chirality : 0.045 0.132 469 Planarity : 0.004 0.048 565 Dihedral : 4.034 12.899 440 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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 are not related in a simple way. whole: -0.15 (0.45), residues: 392 helix: -3.27 (0.86), residues: 24 sheet: 0.46 (0.45), residues: 154 loop : -0.03 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 357 TYR 0.008 0.001 TYR E 453 PHE 0.012 0.001 PHE B 73 TRP 0.011 0.001 TRP E 436 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 3202) covalent geometry : angle 0.58844 / 0.31 ( 4352) SS BOND : bond 0.00510 / 0.25 ( 4) SS BOND : angle 0.79091 / 0.47 ( 8) hydrogen bonds : bond 0.03490 / 2.41 ( 85) hydrogen bonds : angle 4.90078 / 3.28 ( 198) link_NAG-ASN : bond 0.00129 / 0.07 ( 1) link_NAG-ASN : angle 0.80684 / 0.43 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 784 Ramachandran restraints generated. 392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8220 (tp40) cc_final: 0.7807 (mm-40) REVERT: B 91 CYS cc_start: 0.8907 (t) cc_final: 0.8353 (p) REVERT: E 370 ASN cc_start: 0.7019 (p0) cc_final: 0.6807 (p0) REVERT: E 474 GLN cc_start: 0.7799 (pp30) cc_final: 0.7584 (pp30) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0754 time to fit residues: 6.7972 Evaluate side-chains 65 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 0.0020 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.0050 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.140737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.129956 restraints weight = 4345.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.120149 restraints weight = 8360.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.115732 restraints weight = 7101.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.116766 restraints weight = 8508.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.116649 restraints weight = 5753.722| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3207 Z= 0.105 Angle : 0.569 4.839 4363 Z= 0.297 Chirality : 0.044 0.130 469 Planarity : 0.004 0.047 565 Dihedral : 3.922 13.042 440 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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 are not related in a simple way. whole: -0.06 (0.44), residues: 392 helix: -3.26 (0.84), residues: 24 sheet: 0.61 (0.45), residues: 152 loop : -0.04 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 357 TYR 0.007 0.001 TYR B 36 PHE 0.011 0.001 PHE B 73 TRP 0.011 0.001 TRP E 436 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 3202) covalent geometry : angle 0.56866 / 0.30 ( 4352) SS BOND : bond 0.00441 / 0.21 ( 4) SS BOND : angle 0.70187 / 0.45 ( 8) hydrogen bonds : bond 0.03238 / 2.27 ( 85) hydrogen bonds : angle 4.84490 / 3.27 ( 198) link_NAG-ASN : bond 0.00139 / 0.07 ( 1) link_NAG-ASN : angle 0.76238 / 0.40 ( 3) =============================================================================== Job complete usr+sys time: 822.41 seconds wall clock time: 14 minutes 49.31 seconds (889.31 seconds total)