Starting phenix.real_space_refine on Fri Aug 22 13:17:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvm_34132/08_2025/7yvm_34132.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvm_34132/08_2025/7yvm_34132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvm_34132/08_2025/7yvm_34132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvm_34132/08_2025/7yvm_34132.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvm_34132/08_2025/7yvm_34132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvm_34132/08_2025/7yvm_34132.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 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 1991 2.51 5 N 528 2.21 5 O 591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3126 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1435 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 4, 'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 80 Time building chain proxies: 0.83, per 1000 atoms: 0.27 Number of scatterers: 3126 At special positions: 0 Unit cell: (62.32, 72.16, 100.04, 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 591 8.00 N 528 7.00 C 1991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.06 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.09 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 96.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 9.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.134A pdb=" N SER A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 86 through 90 removed outlier: 4.139A pdb=" N THR C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.838A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 3.821A pdb=" N GLU A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.680A pdb=" N LEU A 11 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 85 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU A 33 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TYR A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.998A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.998A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR C 107 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.667A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 106 hydrogen bonds defined for protein. 252 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.35 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 505 1.31 - 1.44: 942 1.44 - 1.58: 1737 1.58 - 1.71: 0 1.71 - 1.85: 20 Bond restraints: 3204 Sorted by residual: bond pdb=" C TYR C 33 " pdb=" O TYR C 33 " ideal model delta sigma weight residual 1.235 1.172 0.063 1.26e-02 6.30e+03 2.50e+01 bond pdb=" C PRO A 95 " pdb=" O PRO A 95 " ideal model delta sigma weight residual 1.240 1.186 0.055 1.12e-02 7.97e+03 2.39e+01 bond pdb=" N GLY A 101 " pdb=" CA GLY A 101 " ideal model delta sigma weight residual 1.442 1.479 -0.037 7.70e-03 1.69e+04 2.30e+01 bond pdb=" CA ASN A 93 " pdb=" C ASN A 93 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.28e-02 6.10e+03 2.16e+01 bond pdb=" C THR A 99 " pdb=" O THR A 99 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.13e-02 7.83e+03 1.90e+01 ... (remaining 3199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 4287 4.04 - 8.08: 70 8.08 - 12.12: 8 12.12 - 16.16: 1 16.16 - 20.20: 3 Bond angle restraints: 4369 Sorted by residual: angle pdb=" C PRO A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta sigma weight residual 119.84 138.11 -18.27 1.25e+00 6.40e-01 2.14e+02 angle pdb=" N PRO B 521 " pdb=" CA PRO B 521 " pdb=" C PRO B 521 " ideal model delta sigma weight residual 112.33 92.13 20.20 1.87e+00 2.86e-01 1.17e+02 angle pdb=" C TYR A 98 " pdb=" CA TYR A 98 " pdb=" CB TYR A 98 " ideal model delta sigma weight residual 109.99 93.12 16.87 1.61e+00 3.86e-01 1.10e+02 angle pdb=" C ARG C 97 " pdb=" CA ARG C 97 " pdb=" CB ARG C 97 " ideal model delta sigma weight residual 111.23 99.22 12.01 1.68e+00 3.54e-01 5.11e+01 angle pdb=" C ARG B 454 " pdb=" CA ARG B 454 " pdb=" CB ARG B 454 " ideal model delta sigma weight residual 110.19 99.37 10.82 1.62e+00 3.81e-01 4.46e+01 ... (remaining 4364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.11: 1776 24.11 - 48.22: 86 48.22 - 72.32: 10 72.32 - 96.43: 0 96.43 - 120.54: 1 Dihedral angle restraints: 1873 sinusoidal: 667 harmonic: 1206 Sorted by residual: dihedral pdb=" CA PRO A 95 " pdb=" C PRO A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual -180.00 -59.46 -120.54 0 5.00e+00 4.00e-02 5.81e+02 dihedral pdb=" C TRP A 94 " pdb=" N TRP A 94 " pdb=" CA TRP A 94 " pdb=" CB TRP A 94 " ideal model delta harmonic sigma weight residual -122.60 -151.47 28.87 0 2.50e+00 1.60e-01 1.33e+02 dihedral pdb=" N TRP A 94 " pdb=" C TRP A 94 " pdb=" CA TRP A 94 " pdb=" CB TRP A 94 " ideal model delta harmonic sigma weight residual 122.80 151.58 -28.78 0 2.50e+00 1.60e-01 1.33e+02 ... (remaining 1870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.252: 476 0.252 - 0.504: 5 0.504 - 0.757: 0 0.757 - 1.009: 0 1.009 - 1.261: 1 Chirality restraints: 482 Sorted by residual: chirality pdb=" CA TRP A 94 " pdb=" N TRP A 94 " pdb=" C TRP A 94 " pdb=" CB TRP A 94 " both_signs ideal model delta sigma weight residual False 2.51 1.25 1.26 2.00e-01 2.50e+01 3.97e+01 chirality pdb=" CA CYS C 95 " pdb=" N CYS C 95 " pdb=" C CYS C 95 " pdb=" CB CYS C 95 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" CA TYR A 98 " pdb=" N TYR A 98 " pdb=" C TYR A 98 " pdb=" CB TYR A 98 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 479 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 90 " -0.036 2.00e-02 2.50e+03 7.38e-02 5.45e+01 pdb=" C GLN A 90 " 0.128 2.00e-02 2.50e+03 pdb=" O GLN A 90 " -0.047 2.00e-02 2.50e+03 pdb=" N TYR A 91 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 94 " -0.086 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO A 95 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 94 " 0.049 2.00e-02 2.50e+03 2.66e-02 1.77e+01 pdb=" CG TRP A 94 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 94 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 94 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 94 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 94 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 94 " -0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 94 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 94 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A 94 " 0.017 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 205 2.71 - 3.26: 3153 3.26 - 3.81: 4790 3.81 - 4.35: 5932 4.35 - 4.90: 9876 Nonbonded interactions: 23956 Sorted by model distance: nonbonded pdb=" OH TYR A 98 " pdb=" OG1 THR C 105 " model vdw 2.166 3.040 nonbonded pdb=" O SER A 77 " pdb=" NE2 GLN A 79 " model vdw 2.275 3.120 nonbonded pdb=" NH1 ARG C 66 " pdb=" O ASN C 83 " model vdw 2.349 3.120 nonbonded pdb=" O LEU B 518 " pdb=" C HIS B 519 " model vdw 2.357 3.270 nonbonded pdb=" SD MET A 4 " pdb=" OE1 GLN A 90 " model vdw 2.363 3.400 ... (remaining 23951 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: 8.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.080 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.009 0.063 3210 Z= 0.609 Angle : 1.769 55.464 4381 Z= 1.007 Chirality : 0.092 1.261 482 Planarity : 0.009 0.134 566 Dihedral : 13.483 120.539 1091 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 28.59 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.18 % Favored : 90.34 % Rotamer: Outliers : 1.57 % Allowed : 7.55 % Favored : 90.88 % Cbeta Deviations : 1.57 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.19 (0.34), residues: 414 helix: -4.90 (0.26), residues: 21 sheet: -1.69 (0.41), residues: 127 loop : -3.36 (0.31), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 357 TYR 0.044 0.003 TYR B 380 PHE 0.034 0.003 PHE B 347 TRP 0.055 0.008 TRP C 47 HIS 0.001 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00939 ( 3204) covalent geometry : angle 1.37741 ( 4369) SS BOND : bond 0.03015 ( 6) SS BOND : angle 21.26120 ( 12) hydrogen bonds : bond 0.15734 ( 102) hydrogen bonds : angle 7.94963 ( 252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8297 (mp) cc_final: 0.7834 (mt) REVERT: C 59 TYR cc_start: 0.8050 (m-80) cc_final: 0.7160 (m-80) REVERT: B 432 CYS cc_start: 0.5883 (p) cc_final: 0.4893 (p) outliers start: 5 outliers final: 3 residues processed: 106 average time/residue: 0.0564 time to fit residues: 7.1055 Evaluate side-chains 60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 95 PRO Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.0570 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN B 422 ASN B 493 GLN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.146220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.129735 restraints weight = 6616.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.132675 restraints weight = 3770.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.134624 restraints weight = 2537.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.135948 restraints weight = 1908.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.136678 restraints weight = 1554.677| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 3210 Z= 0.172 Angle : 0.787 10.469 4381 Z= 0.404 Chirality : 0.048 0.245 482 Planarity : 0.006 0.085 566 Dihedral : 5.971 52.407 466 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.59 % Favored : 94.93 % Rotamer: Outliers : 3.46 % Allowed : 16.67 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.38), residues: 414 helix: -3.68 (0.70), residues: 23 sheet: -1.06 (0.43), residues: 127 loop : -2.17 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 19 TYR 0.021 0.002 TYR A 49 PHE 0.016 0.002 PHE B 400 TRP 0.022 0.003 TRP C 47 HIS 0.002 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 3204) covalent geometry : angle 0.77013 ( 4369) SS BOND : bond 0.00413 ( 6) SS BOND : angle 3.21417 ( 12) hydrogen bonds : bond 0.04051 ( 102) hydrogen bonds : angle 6.60967 ( 252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8343 (mp) cc_final: 0.7906 (mt) REVERT: A 70 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6866 (mp0) REVERT: C 59 TYR cc_start: 0.7914 (m-80) cc_final: 0.7073 (m-80) REVERT: B 418 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8477 (mt) outliers start: 11 outliers final: 6 residues processed: 73 average time/residue: 0.0564 time to fit residues: 4.9024 Evaluate side-chains 65 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 432 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.144288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.127292 restraints weight = 6669.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.130246 restraints weight = 3851.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.132191 restraints weight = 2627.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.133492 restraints weight = 1995.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.134371 restraints weight = 1637.512| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3210 Z= 0.154 Angle : 0.695 8.507 4381 Z= 0.359 Chirality : 0.046 0.216 482 Planarity : 0.006 0.067 566 Dihedral : 5.236 50.943 458 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.28 % Favored : 93.48 % Rotamer: Outliers : 4.40 % Allowed : 20.75 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.39), residues: 414 helix: -2.32 (0.99), residues: 23 sheet: -0.76 (0.42), residues: 134 loop : -1.72 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 19 TYR 0.017 0.001 TYR A 49 PHE 0.029 0.002 PHE B 392 TRP 0.013 0.002 TRP C 47 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3204) covalent geometry : angle 0.68126 ( 4369) SS BOND : bond 0.00449 ( 6) SS BOND : angle 2.66814 ( 12) hydrogen bonds : bond 0.03839 ( 102) hydrogen bonds : angle 6.03874 ( 252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8431 (mp) cc_final: 0.8006 (mt) REVERT: A 70 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7000 (mp0) REVERT: C 59 TYR cc_start: 0.7903 (m-80) cc_final: 0.7165 (m-80) REVERT: B 351 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.6737 (t80) REVERT: B 418 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8512 (mt) REVERT: B 436 TRP cc_start: 0.6767 (OUTLIER) cc_final: 0.5912 (m-10) outliers start: 14 outliers final: 5 residues processed: 73 average time/residue: 0.0589 time to fit residues: 5.1058 Evaluate side-chains 66 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 436 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.141233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.124304 restraints weight = 6671.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.127250 restraints weight = 3836.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.129192 restraints weight = 2603.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.130464 restraints weight = 1973.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.131337 restraints weight = 1617.903| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 3210 Z= 0.192 Angle : 0.778 15.483 4381 Z= 0.402 Chirality : 0.046 0.263 482 Planarity : 0.006 0.077 566 Dihedral : 5.553 49.295 458 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.28 % Favored : 93.48 % Rotamer: Outliers : 6.92 % Allowed : 20.13 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.40), residues: 414 helix: -1.87 (0.96), residues: 21 sheet: -0.26 (0.44), residues: 138 loop : -1.83 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 357 TYR 0.015 0.002 TYR A 49 PHE 0.035 0.003 PHE B 377 TRP 0.014 0.002 TRP B 353 HIS 0.001 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 3204) covalent geometry : angle 0.76663 ( 4369) SS BOND : bond 0.00579 ( 6) SS BOND : angle 2.68644 ( 12) hydrogen bonds : bond 0.04070 ( 102) hydrogen bonds : angle 6.16582 ( 252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8504 (mp) cc_final: 0.8019 (mt) REVERT: A 70 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7047 (mp0) REVERT: A 79 GLN cc_start: 0.7172 (mp10) cc_final: 0.6618 (mp10) REVERT: C 59 TYR cc_start: 0.7957 (m-80) cc_final: 0.7206 (m-80) REVERT: B 351 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.6925 (t80) REVERT: B 436 TRP cc_start: 0.6969 (OUTLIER) cc_final: 0.6094 (m-10) outliers start: 22 outliers final: 13 residues processed: 75 average time/residue: 0.0519 time to fit residues: 4.6599 Evaluate side-chains 72 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 5 optimal weight: 4.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.142717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.126658 restraints weight = 6601.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129386 restraints weight = 3849.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.131269 restraints weight = 2647.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.132369 restraints weight = 2009.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.133273 restraints weight = 1672.467| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3210 Z= 0.169 Angle : 0.744 14.496 4381 Z= 0.381 Chirality : 0.045 0.235 482 Planarity : 0.005 0.068 566 Dihedral : 5.262 49.373 458 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 6.29 % Allowed : 22.96 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.40), residues: 414 helix: -1.86 (0.96), residues: 23 sheet: -0.28 (0.43), residues: 143 loop : -1.79 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.014 0.001 TYR A 49 PHE 0.021 0.002 PHE B 392 TRP 0.011 0.002 TRP B 353 HIS 0.001 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 3204) covalent geometry : angle 0.73503 ( 4369) SS BOND : bond 0.00821 ( 6) SS BOND : angle 2.27080 ( 12) hydrogen bonds : bond 0.03876 ( 102) hydrogen bonds : angle 5.95930 ( 252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8543 (mp) cc_final: 0.8088 (mt) REVERT: A 79 GLN cc_start: 0.7095 (mp10) cc_final: 0.6546 (mp10) REVERT: C 59 TYR cc_start: 0.7916 (m-80) cc_final: 0.7199 (m-80) REVERT: B 351 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.6927 (t80) REVERT: B 436 TRP cc_start: 0.6932 (OUTLIER) cc_final: 0.6045 (m-10) outliers start: 20 outliers final: 14 residues processed: 76 average time/residue: 0.0472 time to fit residues: 4.3393 Evaluate side-chains 71 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 0.0060 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 0.0670 chunk 14 optimal weight: 0.2980 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.144633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.127473 restraints weight = 6704.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.130366 restraints weight = 3885.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.132335 restraints weight = 2666.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.133654 restraints weight = 2035.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.134455 restraints weight = 1673.289| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3210 Z= 0.126 Angle : 0.682 13.877 4381 Z= 0.348 Chirality : 0.044 0.211 482 Planarity : 0.005 0.060 566 Dihedral : 4.823 44.102 458 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 6.29 % Allowed : 23.90 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.40), residues: 414 helix: -1.64 (1.00), residues: 23 sheet: -0.11 (0.44), residues: 142 loop : -1.71 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 66 TYR 0.012 0.001 TYR A 49 PHE 0.017 0.002 PHE B 392 TRP 0.008 0.001 TRP C 47 HIS 0.001 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3204) covalent geometry : angle 0.67524 ( 4369) SS BOND : bond 0.00788 ( 6) SS BOND : angle 2.00559 ( 12) hydrogen bonds : bond 0.03513 ( 102) hydrogen bonds : angle 5.58301 ( 252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8534 (mp) cc_final: 0.8072 (mt) REVERT: A 79 GLN cc_start: 0.7032 (mp10) cc_final: 0.6446 (mp10) REVERT: C 59 TYR cc_start: 0.7910 (m-80) cc_final: 0.7211 (m-80) REVERT: B 351 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.6907 (t80) REVERT: B 436 TRP cc_start: 0.6728 (OUTLIER) cc_final: 0.6346 (m-10) outliers start: 20 outliers final: 13 residues processed: 84 average time/residue: 0.0491 time to fit residues: 4.9860 Evaluate side-chains 72 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.143935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125711 restraints weight = 6605.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.128736 restraints weight = 3928.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.130788 restraints weight = 2723.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.132203 restraints weight = 2089.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.133044 restraints weight = 1714.867| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3210 Z= 0.156 Angle : 0.728 13.978 4381 Z= 0.372 Chirality : 0.044 0.221 482 Planarity : 0.005 0.063 566 Dihedral : 5.047 45.214 458 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 5.97 % Allowed : 23.90 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.40), residues: 414 helix: -1.44 (1.03), residues: 23 sheet: -0.13 (0.43), residues: 143 loop : -1.76 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 346 TYR 0.012 0.001 TYR A 49 PHE 0.014 0.002 PHE C 67 TRP 0.011 0.001 TRP C 47 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3204) covalent geometry : angle 0.72054 ( 4369) SS BOND : bond 0.00792 ( 6) SS BOND : angle 2.05540 ( 12) hydrogen bonds : bond 0.03775 ( 102) hydrogen bonds : angle 5.61324 ( 252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8589 (mp) cc_final: 0.8147 (mt) REVERT: A 79 GLN cc_start: 0.7136 (mp10) cc_final: 0.6481 (mp10) REVERT: C 59 TYR cc_start: 0.7981 (m-80) cc_final: 0.7312 (m-80) REVERT: B 351 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.7004 (t80) REVERT: B 436 TRP cc_start: 0.6760 (OUTLIER) cc_final: 0.6477 (m-10) outliers start: 19 outliers final: 16 residues processed: 73 average time/residue: 0.0523 time to fit residues: 4.6014 Evaluate side-chains 73 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.143645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.125568 restraints weight = 6701.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.128397 restraints weight = 4042.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.130346 restraints weight = 2832.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.131572 restraints weight = 2189.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.132511 restraints weight = 1828.652| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 3210 Z= 0.168 Angle : 0.734 13.996 4381 Z= 0.378 Chirality : 0.045 0.222 482 Planarity : 0.005 0.061 566 Dihedral : 5.085 44.684 458 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 7.23 % Allowed : 22.96 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.40), residues: 414 helix: -1.40 (1.03), residues: 23 sheet: -0.30 (0.42), residues: 152 loop : -1.77 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 24 TYR 0.012 0.001 TYR A 49 PHE 0.022 0.002 PHE B 392 TRP 0.011 0.002 TRP C 47 HIS 0.001 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 3204) covalent geometry : angle 0.72612 ( 4369) SS BOND : bond 0.00805 ( 6) SS BOND : angle 2.12695 ( 12) hydrogen bonds : bond 0.03885 ( 102) hydrogen bonds : angle 5.68346 ( 252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8601 (mp) cc_final: 0.8133 (mt) REVERT: A 79 GLN cc_start: 0.7082 (mp10) cc_final: 0.6509 (mp10) REVERT: C 59 TYR cc_start: 0.8023 (m-80) cc_final: 0.7275 (m-80) REVERT: B 351 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.7036 (t80) REVERT: B 436 TRP cc_start: 0.6775 (OUTLIER) cc_final: 0.6451 (m-10) outliers start: 23 outliers final: 20 residues processed: 73 average time/residue: 0.0570 time to fit residues: 5.0765 Evaluate side-chains 74 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 0.0370 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.142172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.124126 restraints weight = 6574.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127013 restraints weight = 3930.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.128971 restraints weight = 2740.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.130232 restraints weight = 2111.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.131171 restraints weight = 1756.190| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 3210 Z= 0.183 Angle : 0.763 13.465 4381 Z= 0.393 Chirality : 0.045 0.223 482 Planarity : 0.005 0.063 566 Dihedral : 5.224 44.607 458 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 6.92 % Allowed : 25.16 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.39), residues: 414 helix: -1.13 (1.07), residues: 21 sheet: -0.23 (0.42), residues: 144 loop : -1.95 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.013 0.001 TYR A 98 PHE 0.021 0.002 PHE B 392 TRP 0.011 0.002 TRP C 47 HIS 0.001 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 3204) covalent geometry : angle 0.75670 ( 4369) SS BOND : bond 0.00757 ( 6) SS BOND : angle 2.06816 ( 12) hydrogen bonds : bond 0.04100 ( 102) hydrogen bonds : angle 5.80657 ( 252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8530 (mp) cc_final: 0.8071 (mt) REVERT: A 79 GLN cc_start: 0.7149 (mp10) cc_final: 0.6598 (mp10) REVERT: C 59 TYR cc_start: 0.8094 (m-80) cc_final: 0.7358 (m-80) REVERT: B 351 TYR cc_start: 0.7587 (OUTLIER) cc_final: 0.6975 (t80) REVERT: B 374 PHE cc_start: 0.4207 (m-10) cc_final: 0.3888 (m-80) REVERT: B 436 TRP cc_start: 0.6929 (OUTLIER) cc_final: 0.6449 (m-10) outliers start: 22 outliers final: 20 residues processed: 69 average time/residue: 0.0501 time to fit residues: 4.1927 Evaluate side-chains 74 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 0.0370 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.144284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.126344 restraints weight = 6487.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.129166 restraints weight = 3889.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.131094 restraints weight = 2727.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.132226 restraints weight = 2114.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.133185 restraints weight = 1783.897| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3210 Z= 0.154 Angle : 0.743 13.104 4381 Z= 0.383 Chirality : 0.044 0.218 482 Planarity : 0.005 0.057 566 Dihedral : 5.040 43.179 458 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 6.92 % Allowed : 25.79 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.39), residues: 414 helix: -1.05 (1.08), residues: 21 sheet: -0.18 (0.43), residues: 142 loop : -1.94 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 66 TYR 0.012 0.001 TYR A 49 PHE 0.014 0.002 PHE B 374 TRP 0.009 0.001 TRP C 47 HIS 0.001 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3204) covalent geometry : angle 0.73745 ( 4369) SS BOND : bond 0.00716 ( 6) SS BOND : angle 1.84443 ( 12) hydrogen bonds : bond 0.03878 ( 102) hydrogen bonds : angle 5.69393 ( 252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8420 (mp) cc_final: 0.7978 (mt) REVERT: A 24 ARG cc_start: 0.7804 (tmm-80) cc_final: 0.7292 (ttp80) REVERT: A 79 GLN cc_start: 0.7072 (mp10) cc_final: 0.6649 (mp10) REVERT: C 59 TYR cc_start: 0.8069 (m-80) cc_final: 0.7328 (m-80) REVERT: B 351 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.6896 (t80) REVERT: B 374 PHE cc_start: 0.4080 (m-10) cc_final: 0.3797 (m-80) REVERT: B 436 TRP cc_start: 0.6867 (OUTLIER) cc_final: 0.6459 (m-10) outliers start: 22 outliers final: 18 residues processed: 69 average time/residue: 0.0607 time to fit residues: 5.0125 Evaluate side-chains 72 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.141369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.123308 restraints weight = 6735.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.126210 restraints weight = 4029.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.128156 restraints weight = 2798.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129407 restraints weight = 2160.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.129939 restraints weight = 1806.480| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 3210 Z= 0.222 Angle : 0.800 13.280 4381 Z= 0.416 Chirality : 0.046 0.234 482 Planarity : 0.005 0.062 566 Dihedral : 5.490 44.168 458 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 6.60 % Allowed : 24.21 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.39), residues: 414 helix: -1.23 (1.01), residues: 21 sheet: -0.33 (0.42), residues: 143 loop : -2.09 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.018 0.002 TYR A 98 PHE 0.018 0.002 PHE C 67 TRP 0.012 0.002 TRP B 436 HIS 0.001 0.000 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 3204) covalent geometry : angle 0.79303 ( 4369) SS BOND : bond 0.00723 ( 6) SS BOND : angle 2.18995 ( 12) hydrogen bonds : bond 0.04442 ( 102) hydrogen bonds : angle 5.96507 ( 252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 807.90 seconds wall clock time: 14 minutes 39.98 seconds (879.98 seconds total)