Starting phenix.real_space_refine on Sat Apr 26 19:10:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bg6_16024/04_2025/8bg6_16024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bg6_16024/04_2025/8bg6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bg6_16024/04_2025/8bg6_16024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bg6_16024/04_2025/8bg6_16024.map" model { file = "/net/cci-nas-00/data/ceres_data/8bg6_16024/04_2025/8bg6_16024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bg6_16024/04_2025/8bg6_16024.cif" } resolution = 4.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.83, per 1000 atoms: 0.91 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: 0.64 Conformation dependent library (CDL) restraints added in 343.9 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: 0.36 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: 0.71 Time building geometry restraints manager: 0.78 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: 1706 15.98 - 31.95: 144 31.95 - 47.93: 39 47.93 - 63.91: 5 63.91 - 79.88: 2 Dihedral angle restraints: 1896 sinusoidal: 746 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 1893 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 12.582 79.885 1156 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP E 436 HIS 0.006 0.002 HIS B 90 PHE 0.011 0.001 PHE E 400 TYR 0.014 0.001 TYR E 473 ARG 0.002 0.000 ARG B 61 Details of bonding type rmsd link_NAG-ASN : bond 0.04698 ( 1) link_NAG-ASN : angle 3.35730 ( 3) hydrogen bonds : bond 0.22035 ( 85) hydrogen bonds : angle 6.05639 ( 198) SS BOND : bond 0.04397 ( 4) SS BOND : angle 3.69740 ( 8) covalent geometry : bond 0.00602 ( 3202) covalent geometry : angle 0.93687 ( 4352) *********************** 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 : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1587 time to fit residues: 15.5247 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 : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3539 r_free = 0.3539 target = 0.144183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.120520 restraints weight = 4366.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.118731 restraints weight = 5780.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.116545 restraints weight = 5979.820| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3207 Z= 0.118 Angle : 0.566 5.110 4363 Z= 0.301 Chirality : 0.045 0.136 469 Planarity : 0.004 0.035 565 Dihedral : 4.069 14.608 461 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.44), residues: 392 helix: -3.43 (0.95), residues: 18 sheet: 0.62 (0.50), residues: 127 loop : -0.41 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 436 HIS 0.003 0.001 HIS B 90 PHE 0.010 0.001 PHE E 490 TYR 0.014 0.001 TYR E 453 ARG 0.004 0.000 ARG E 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 1) link_NAG-ASN : angle 0.67054 ( 3) hydrogen bonds : bond 0.03992 ( 85) hydrogen bonds : angle 5.14586 ( 198) SS BOND : bond 0.00804 ( 4) SS BOND : angle 1.13328 ( 8) covalent geometry : bond 0.00259 ( 3202) covalent geometry : angle 0.56468 ( 4352) *********************** 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 : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8286 (t0) cc_final: 0.8078 (t0) REVERT: A 88 GLU cc_start: 0.7391 (tp30) cc_final: 0.7063 (tp30) REVERT: E 370 ASN cc_start: 0.7915 (p0) cc_final: 0.7695 (p0) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1679 time to fit residues: 16.6142 Evaluate side-chains 64 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 0.0060 chunk 4 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3587 r_free = 0.3587 target = 0.146872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135834 restraints weight = 4298.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.129231 restraints weight = 7936.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.123605 restraints weight = 8233.907| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3207 Z= 0.109 Angle : 0.531 4.952 4363 Z= 0.284 Chirality : 0.044 0.131 469 Planarity : 0.004 0.036 565 Dihedral : 3.914 13.861 461 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.44), residues: 392 helix: -3.35 (0.97), residues: 18 sheet: 0.64 (0.50), residues: 126 loop : -0.20 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 436 HIS 0.003 0.001 HIS B 90 PHE 0.011 0.001 PHE B 73 TYR 0.010 0.001 TYR B 36 ARG 0.004 0.000 ARG B 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 1) link_NAG-ASN : angle 0.74731 ( 3) hydrogen bonds : bond 0.03873 ( 85) hydrogen bonds : angle 4.89820 ( 198) SS BOND : bond 0.00504 ( 4) SS BOND : angle 0.94194 ( 8) covalent geometry : bond 0.00235 ( 3202) covalent geometry : angle 0.53020 ( 4352) *********************** 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 80 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8263 (t0) cc_final: 0.7959 (t0) REVERT: A 88 GLU cc_start: 0.7301 (tp30) cc_final: 0.7027 (tp30) REVERT: E 370 ASN cc_start: 0.7925 (p0) cc_final: 0.7646 (p0) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1381 time to fit residues: 13.6211 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 : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.0050 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3587 r_free = 0.3587 target = 0.146779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.136863 restraints weight = 4389.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.132537 restraints weight = 6753.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.126495 restraints weight = 6759.036| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3207 Z= 0.112 Angle : 0.531 5.357 4363 Z= 0.282 Chirality : 0.045 0.173 469 Planarity : 0.004 0.040 565 Dihedral : 3.934 13.013 461 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.44), residues: 392 helix: -3.16 (0.91), residues: 24 sheet: 0.77 (0.50), residues: 126 loop : -0.06 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 36 HIS 0.002 0.001 HIS B 90 PHE 0.010 0.001 PHE B 73 TYR 0.010 0.001 TYR E 453 ARG 0.001 0.000 ARG E 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 1) link_NAG-ASN : angle 0.82783 ( 3) hydrogen bonds : bond 0.03643 ( 85) hydrogen bonds : angle 4.86576 ( 198) SS BOND : bond 0.00670 ( 4) SS BOND : angle 0.95197 ( 8) covalent geometry : bond 0.00242 ( 3202) covalent geometry : angle 0.52979 ( 4352) *********************** 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 : 0.354 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8304 (t0) cc_final: 0.7998 (t0) REVERT: A 88 GLU cc_start: 0.7439 (tp30) cc_final: 0.7218 (tp30) REVERT: B 79 GLN cc_start: 0.8736 (mp10) cc_final: 0.8528 (mp10) REVERT: B 91 CYS cc_start: 0.8771 (t) cc_final: 0.8502 (p) REVERT: E 370 ASN cc_start: 0.7508 (p0) cc_final: 0.7253 (p0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1521 time to fit residues: 15.1660 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 : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 32 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.135890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.123247 restraints weight = 4390.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.117852 restraints weight = 8817.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.112829 restraints weight = 6557.709| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3207 Z= 0.158 Angle : 0.577 5.814 4363 Z= 0.308 Chirality : 0.045 0.137 469 Planarity : 0.004 0.039 565 Dihedral : 4.113 14.282 461 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.10 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.44), residues: 392 helix: -2.90 (0.82), residues: 30 sheet: 0.78 (0.49), residues: 129 loop : -0.21 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 36 HIS 0.005 0.001 HIS B 53 PHE 0.011 0.002 PHE B 73 TYR 0.012 0.002 TYR E 453 ARG 0.004 0.001 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 1) link_NAG-ASN : angle 0.97739 ( 3) hydrogen bonds : bond 0.04281 ( 85) hydrogen bonds : angle 5.21669 ( 198) SS BOND : bond 0.00819 ( 4) SS BOND : angle 1.23758 ( 8) covalent geometry : bond 0.00369 ( 3202) covalent geometry : angle 0.57503 ( 4352) *********************** 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 76 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8129 (tp-100) cc_final: 0.7909 (mm-40) REVERT: E 370 ASN cc_start: 0.7881 (p0) cc_final: 0.7575 (p0) REVERT: E 400 PHE cc_start: 0.7760 (m-80) cc_final: 0.7485 (m-80) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1742 time to fit residues: 15.8340 Evaluate side-chains 67 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 13 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.142467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.130618 restraints weight = 4497.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130820 restraints weight = 9163.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.128577 restraints weight = 6256.445| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3207 Z= 0.152 Angle : 0.583 5.460 4363 Z= 0.312 Chirality : 0.046 0.134 469 Planarity : 0.004 0.043 565 Dihedral : 4.110 13.940 461 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.44), residues: 392 helix: -3.22 (0.90), residues: 24 sheet: 0.66 (0.46), residues: 143 loop : -0.10 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 36 HIS 0.003 0.001 HIS B 90 PHE 0.015 0.001 PHE A 67 TYR 0.012 0.002 TYR B 36 ARG 0.002 0.000 ARG B 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00145 ( 1) link_NAG-ASN : angle 0.92224 ( 3) hydrogen bonds : bond 0.04131 ( 85) hydrogen bonds : angle 5.27379 ( 198) SS BOND : bond 0.00712 ( 4) SS BOND : angle 1.04168 ( 8) covalent geometry : bond 0.00356 ( 3202) covalent geometry : angle 0.58192 ( 4352) *********************** 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 75 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7887 (mm-40) REVERT: E 370 ASN cc_start: 0.6986 (p0) cc_final: 0.6770 (p0) REVERT: E 400 PHE cc_start: 0.7781 (m-80) cc_final: 0.7449 (m-80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1853 time to fit residues: 16.3891 Evaluate side-chains 64 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.138329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.109291 restraints weight = 4365.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.107829 restraints weight = 4671.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.107645 restraints weight = 4791.339| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3207 Z= 0.118 Angle : 0.561 5.365 4363 Z= 0.295 Chirality : 0.044 0.130 469 Planarity : 0.004 0.044 565 Dihedral : 3.945 13.668 461 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.44), residues: 392 helix: -3.24 (0.88), residues: 24 sheet: 0.69 (0.46), residues: 143 loop : -0.02 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 36 HIS 0.005 0.001 HIS B 90 PHE 0.011 0.001 PHE B 73 TYR 0.009 0.001 TYR E 453 ARG 0.004 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00190 ( 1) link_NAG-ASN : angle 0.84467 ( 3) hydrogen bonds : bond 0.03738 ( 85) hydrogen bonds : angle 5.02936 ( 198) SS BOND : bond 0.00535 ( 4) SS BOND : angle 0.77645 ( 8) covalent geometry : bond 0.00274 ( 3202) covalent geometry : angle 0.55996 ( 4352) *********************** 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 77 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7928 (mm-40) REVERT: E 370 ASN cc_start: 0.8471 (p0) cc_final: 0.8253 (p0) REVERT: E 506 GLN cc_start: 0.8907 (mp-120) cc_final: 0.8487 (mp-120) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1798 time to fit residues: 16.3531 Evaluate side-chains 59 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.144599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.131694 restraints weight = 4400.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.127799 restraints weight = 9189.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.123741 restraints weight = 7039.620| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3638 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= 0.120 Angle : 0.581 5.037 4363 Z= 0.305 Chirality : 0.045 0.131 469 Planarity : 0.004 0.045 565 Dihedral : 3.951 13.625 461 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.45), residues: 392 helix: -3.30 (0.86), residues: 24 sheet: 0.48 (0.45), residues: 154 loop : 0.06 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 36 HIS 0.004 0.001 HIS B 90 PHE 0.012 0.001 PHE A 67 TYR 0.009 0.001 TYR B 36 ARG 0.003 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 1) link_NAG-ASN : angle 0.85726 ( 3) hydrogen bonds : bond 0.03668 ( 85) hydrogen bonds : angle 4.99666 ( 198) SS BOND : bond 0.00555 ( 4) SS BOND : angle 0.86327 ( 8) covalent geometry : bond 0.00279 ( 3202) covalent geometry : angle 0.58044 ( 4352) *********************** 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 69 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8122 (tp-100) cc_final: 0.7898 (mm-40) REVERT: E 370 ASN cc_start: 0.7711 (p0) cc_final: 0.7436 (p0) REVERT: E 474 GLN cc_start: 0.7706 (pp30) cc_final: 0.7399 (pp30) REVERT: E 506 GLN cc_start: 0.8956 (mp-120) cc_final: 0.8590 (mp10) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1726 time to fit residues: 14.2046 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 : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.134649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.122820 restraints weight = 4482.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.115390 restraints weight = 8766.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.108528 restraints weight = 7612.325| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3207 Z= 0.195 Angle : 0.652 4.830 4363 Z= 0.349 Chirality : 0.047 0.162 469 Planarity : 0.005 0.045 565 Dihedral : 4.246 14.498 461 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.44), residues: 392 helix: -3.02 (0.77), residues: 30 sheet: 0.44 (0.45), residues: 150 loop : -0.16 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 36 HIS 0.002 0.001 HIS B 53 PHE 0.015 0.002 PHE A 67 TYR 0.013 0.002 TYR B 36 ARG 0.003 0.001 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00027 ( 1) link_NAG-ASN : angle 1.05720 ( 3) hydrogen bonds : bond 0.04636 ( 85) hydrogen bonds : angle 5.41864 ( 198) SS BOND : bond 0.00847 ( 4) SS BOND : angle 1.18015 ( 8) covalent geometry : bond 0.00462 ( 3202) covalent geometry : angle 0.65065 ( 4352) *********************** 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 : 0.327 Fit side-chains revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7929 (mm-40) REVERT: E 370 ASN cc_start: 0.7918 (p0) cc_final: 0.7647 (p0) REVERT: E 465 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7490 (tp30) REVERT: E 474 GLN cc_start: 0.7767 (pp30) cc_final: 0.7422 (pp30) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1834 time to fit residues: 15.4025 Evaluate side-chains 62 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.0040 chunk 1 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.0040 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 overall best weight: 0.4604 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.140922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.114550 restraints weight = 4310.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.114550 restraints weight = 4060.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.114550 restraints weight = 4060.285| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3207 Z= 0.112 Angle : 0.585 5.480 4363 Z= 0.307 Chirality : 0.045 0.130 469 Planarity : 0.004 0.049 565 Dihedral : 3.984 14.126 461 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.45), residues: 392 helix: -3.32 (0.85), residues: 24 sheet: 0.55 (0.45), residues: 153 loop : 0.04 (0.45), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 36 HIS 0.005 0.001 HIS B 90 PHE 0.011 0.001 PHE B 73 TYR 0.008 0.001 TYR E 453 ARG 0.004 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 0.79272 ( 3) hydrogen bonds : bond 0.03497 ( 85) hydrogen bonds : angle 5.08363 ( 198) SS BOND : bond 0.00480 ( 4) SS BOND : angle 0.76880 ( 8) covalent geometry : bond 0.00261 ( 3202) covalent geometry : angle 0.58398 ( 4352) ********************** 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 74 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7061 (mm-40) REVERT: E 370 ASN cc_start: 0.8282 (p0) cc_final: 0.8058 (p0) REVERT: E 465 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7383 (tp30) REVERT: E 474 GLN cc_start: 0.7721 (pp30) cc_final: 0.7460 (pp30) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1659 time to fit residues: 14.6658 Evaluate side-chains 64 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.138970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.109119 restraints weight = 4420.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.109119 restraints weight = 4566.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.109119 restraints weight = 4566.487| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3811 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= 0.107 Angle : 0.570 5.553 4363 Z= 0.299 Chirality : 0.044 0.128 469 Planarity : 0.004 0.048 565 Dihedral : 3.823 13.702 461 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.44), residues: 392 helix: -3.34 (0.84), residues: 24 sheet: 0.89 (0.46), residues: 142 loop : -0.01 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 36 HIS 0.004 0.002 HIS B 90 PHE 0.011 0.001 PHE B 73 TYR 0.007 0.001 TYR B 36 ARG 0.004 0.000 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 1) link_NAG-ASN : angle 0.80002 ( 3) hydrogen bonds : bond 0.03487 ( 85) hydrogen bonds : angle 4.87913 ( 198) SS BOND : bond 0.00469 ( 4) SS BOND : angle 0.74481 ( 8) covalent geometry : bond 0.00247 ( 3202) covalent geometry : angle 0.56963 ( 4352) =============================================================================== Job complete usr+sys time: 1606.48 seconds wall clock time: 28 minutes 32.37 seconds (1712.37 seconds total)