Starting phenix.real_space_refine on Sat Apr 26 18:51:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvm_34132/04_2025/7yvm_34132.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvm_34132/04_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_34132/04_2025/7yvm_34132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvm_34132/04_2025/7yvm_34132.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvm_34132/04_2025/7yvm_34132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvm_34132/04_2025/7yvm_34132.cif" } resolution = 3.5 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 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 Time building chain proxies: 4.57, per 1000 atoms: 1.46 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: 0.68 Conformation dependent library (CDL) restraints added in 361.9 milliseconds 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: 0.39 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: 0.80 Time building geometry restraints manager: 0.84 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: 5.400 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.250 Find NCS groups from input model: 0.040 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.860 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.055 0.008 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.034 0.003 PHE B 347 TYR 0.044 0.003 TYR B 380 ARG 0.010 0.001 ARG B 357 Details of bonding type rmsd hydrogen bonds : bond 0.15734 ( 102) hydrogen bonds : angle 7.94963 ( 252) SS BOND : bond 0.03015 ( 6) SS BOND : angle 21.26120 ( 12) covalent geometry : bond 0.00939 ( 3204) covalent geometry : angle 1.37741 ( 4369) *********************** 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 : 0.343 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: 0.1645 time to fit residues: 20.6176 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 : 0.317 ------------------------------------------------------------------------------- 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 33 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.146977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.130509 restraints weight = 6569.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.133433 restraints weight = 3769.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.135374 restraints weight = 2547.900| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 3210 Z= 0.168 Angle : 0.781 10.916 4381 Z= 0.401 Chirality : 0.048 0.253 482 Planarity : 0.006 0.083 566 Dihedral : 5.962 53.910 466 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.35 % Favored : 95.17 % Rotamer: Outliers : 3.14 % Allowed : 16.35 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -2.82 (0.38), residues: 414 helix: -3.68 (0.70), residues: 23 sheet: -1.20 (0.41), residues: 133 loop : -2.15 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 47 HIS 0.001 0.001 HIS B 519 PHE 0.016 0.002 PHE B 400 TYR 0.020 0.002 TYR A 49 ARG 0.003 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 102) hydrogen bonds : angle 6.60403 ( 252) SS BOND : bond 0.00371 ( 6) SS BOND : angle 3.20443 ( 12) covalent geometry : bond 0.00405 ( 3204) covalent geometry : angle 0.76389 ( 4369) *********************** 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: 10 poor density : 70 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8342 (mp) cc_final: 0.7910 (mt) REVERT: C 59 TYR cc_start: 0.7939 (m-80) cc_final: 0.7098 (m-80) REVERT: B 418 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8457 (mt) outliers start: 10 outliers final: 4 residues processed: 73 average time/residue: 0.1873 time to fit residues: 16.2578 Evaluate side-chains 65 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 B residue 347 PHE Chi-restraints excluded: chain B residue 418 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.145741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.128786 restraints weight = 6596.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.131703 restraints weight = 3849.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.133638 restraints weight = 2634.757| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 3210 Z= 0.159 Angle : 0.730 11.723 4381 Z= 0.374 Chirality : 0.046 0.288 482 Planarity : 0.005 0.064 566 Dihedral : 5.147 49.973 458 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.04 % Favored : 93.72 % Rotamer: Outliers : 4.09 % Allowed : 20.75 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -2.04 (0.39), residues: 414 helix: -1.78 (1.07), residues: 21 sheet: -0.72 (0.42), residues: 133 loop : -1.73 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 47 HIS 0.000 0.000 HIS B 519 PHE 0.029 0.002 PHE B 392 TYR 0.017 0.001 TYR A 49 ARG 0.003 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 102) hydrogen bonds : angle 5.87866 ( 252) SS BOND : bond 0.01153 ( 6) SS BOND : angle 3.41334 ( 12) covalent geometry : bond 0.00387 ( 3204) covalent geometry : angle 0.70859 ( 4369) *********************** 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 81 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8472 (mp) cc_final: 0.8047 (mt) REVERT: A 70 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7002 (mp0) REVERT: C 59 TYR cc_start: 0.7876 (m-80) cc_final: 0.7153 (m-80) REVERT: B 351 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6738 (t80) REVERT: B 436 TRP cc_start: 0.6684 (OUTLIER) cc_final: 0.5756 (m-10) outliers start: 13 outliers final: 6 residues processed: 78 average time/residue: 0.1740 time to fit residues: 16.1889 Evaluate side-chains 69 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 401 VAL 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 18 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 0.0570 chunk 2 optimal weight: 0.0570 chunk 33 optimal weight: 0.8980 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.146378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129533 restraints weight = 6764.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.132282 restraints weight = 3907.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.134173 restraints weight = 2696.599| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3210 Z= 0.128 Angle : 0.679 8.139 4381 Z= 0.349 Chirality : 0.044 0.234 482 Planarity : 0.005 0.070 566 Dihedral : 4.845 41.452 458 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 6.60 % Allowed : 19.81 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.71 (0.41), residues: 414 helix: -2.26 (0.88), residues: 27 sheet: -0.30 (0.44), residues: 138 loop : -1.53 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 94 HIS 0.001 0.000 HIS B 505 PHE 0.018 0.002 PHE B 392 TYR 0.015 0.001 TYR A 49 ARG 0.002 0.000 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 102) hydrogen bonds : angle 5.57885 ( 252) SS BOND : bond 0.00557 ( 6) SS BOND : angle 2.40550 ( 12) covalent geometry : bond 0.00300 ( 3204) covalent geometry : angle 0.66782 ( 4369) *********************** 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 85 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8421 (mp) cc_final: 0.8026 (mt) REVERT: A 70 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7021 (mp0) REVERT: C 59 TYR cc_start: 0.7850 (m-80) cc_final: 0.7191 (m-80) REVERT: B 351 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6680 (t80) REVERT: B 418 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8610 (mt) REVERT: B 436 TRP cc_start: 0.6550 (OUTLIER) cc_final: 0.5643 (m-10) outliers start: 21 outliers final: 11 residues processed: 78 average time/residue: 0.1626 time to fit residues: 15.3419 Evaluate side-chains 70 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 5 VAL 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 401 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP 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 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 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 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 = 0.3983 r_free = 0.3983 target = 0.144568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.127357 restraints weight = 6620.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.130327 restraints weight = 3780.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.132305 restraints weight = 2557.726| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3210 Z= 0.153 Angle : 0.712 14.071 4381 Z= 0.367 Chirality : 0.045 0.237 482 Planarity : 0.005 0.065 566 Dihedral : 4.953 45.898 458 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 6.92 % Allowed : 19.81 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.55 (0.41), residues: 414 helix: -1.19 (1.11), residues: 21 sheet: -0.12 (0.45), residues: 137 loop : -1.59 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 353 HIS 0.001 0.000 HIS B 505 PHE 0.037 0.002 PHE B 377 TYR 0.013 0.001 TYR A 49 ARG 0.003 0.000 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 102) hydrogen bonds : angle 5.61488 ( 252) SS BOND : bond 0.00933 ( 6) SS BOND : angle 2.42772 ( 12) covalent geometry : bond 0.00364 ( 3204) covalent geometry : angle 0.70130 ( 4369) *********************** 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 85 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8560 (mp) cc_final: 0.8110 (mt) REVERT: A 70 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7048 (mp0) REVERT: C 3 GLN cc_start: 0.7785 (pp30) cc_final: 0.7239 (pp30) REVERT: C 59 TYR cc_start: 0.7890 (m-80) cc_final: 0.7248 (m-80) REVERT: B 351 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.6882 (t80) REVERT: B 436 TRP cc_start: 0.6617 (OUTLIER) cc_final: 0.6251 (m-10) outliers start: 22 outliers final: 16 residues processed: 78 average time/residue: 0.1494 time to fit residues: 14.1147 Evaluate side-chains 72 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 A residue 106 LEU Chi-restraints excluded: chain C residue 5 VAL 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 415 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP 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 13 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 0.0370 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.144647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.127311 restraints weight = 6801.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.130240 restraints weight = 3877.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.132281 restraints weight = 2636.594| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 3210 Z= 0.140 Angle : 0.699 13.134 4381 Z= 0.358 Chirality : 0.044 0.210 482 Planarity : 0.005 0.062 566 Dihedral : 4.894 44.345 458 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 6.92 % Allowed : 20.75 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.43 (0.41), residues: 414 helix: -1.83 (1.05), residues: 21 sheet: -0.15 (0.44), residues: 144 loop : -1.39 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.020 0.002 PHE B 392 TYR 0.013 0.001 TYR A 49 ARG 0.003 0.000 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 102) hydrogen bonds : angle 5.55569 ( 252) SS BOND : bond 0.00760 ( 6) SS BOND : angle 2.11788 ( 12) covalent geometry : bond 0.00339 ( 3204) covalent geometry : angle 0.69074 ( 4369) *********************** 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 82 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8524 (mp) cc_final: 0.8047 (mt) REVERT: A 24 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7527 (ttp80) REVERT: C 59 TYR cc_start: 0.7897 (m-80) cc_final: 0.7211 (m-80) REVERT: B 351 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6805 (t80) outliers start: 22 outliers final: 17 residues processed: 77 average time/residue: 0.1472 time to fit residues: 13.8248 Evaluate side-chains 72 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 A residue 99 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain C residue 5 VAL 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 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 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 18 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 3 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 = 0.3991 r_free = 0.3991 target = 0.144901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.128169 restraints weight = 6647.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.130900 restraints weight = 3995.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.132725 restraints weight = 2793.259| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5039 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= 0.142 Angle : 0.706 13.579 4381 Z= 0.359 Chirality : 0.045 0.208 482 Planarity : 0.005 0.059 566 Dihedral : 4.833 42.590 458 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 7.23 % Allowed : 21.38 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.36 (0.41), residues: 414 helix: -1.67 (1.04), residues: 21 sheet: -0.03 (0.44), residues: 144 loop : -1.41 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.018 0.002 PHE B 392 TYR 0.012 0.001 TYR A 49 ARG 0.002 0.000 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 102) hydrogen bonds : angle 5.54380 ( 252) SS BOND : bond 0.00770 ( 6) SS BOND : angle 2.02289 ( 12) covalent geometry : bond 0.00343 ( 3204) covalent geometry : angle 0.69877 ( 4369) *********************** 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 80 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8530 (mp) cc_final: 0.8100 (mt) REVERT: C 59 TYR cc_start: 0.7904 (m-80) cc_final: 0.7197 (m-80) REVERT: B 351 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.6905 (t80) outliers start: 23 outliers final: 19 residues processed: 74 average time/residue: 0.1667 time to fit residues: 15.0464 Evaluate side-chains 73 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 106 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 371 PHE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 434 ILE 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 36 optimal weight: 0.0050 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.0270 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.4652 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.145604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.128274 restraints weight = 6811.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.131209 restraints weight = 3954.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.133176 restraints weight = 2723.742| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3210 Z= 0.132 Angle : 0.700 13.420 4381 Z= 0.359 Chirality : 0.044 0.207 482 Planarity : 0.005 0.056 566 Dihedral : 4.725 41.665 458 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.29 % Allowed : 22.33 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.38 (0.40), residues: 414 helix: -0.23 (1.39), residues: 15 sheet: -0.10 (0.43), residues: 144 loop : -1.51 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.011 0.001 PHE B 400 TYR 0.012 0.001 TYR A 49 ARG 0.006 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 102) hydrogen bonds : angle 5.45604 ( 252) SS BOND : bond 0.00785 ( 6) SS BOND : angle 1.91759 ( 12) covalent geometry : bond 0.00320 ( 3204) covalent geometry : angle 0.69346 ( 4369) *********************** 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 81 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8570 (mp) cc_final: 0.8174 (mt) REVERT: C 3 GLN cc_start: 0.7892 (pp30) cc_final: 0.7493 (pp30) REVERT: C 59 TYR cc_start: 0.7950 (m-80) cc_final: 0.7249 (m-80) REVERT: B 351 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6835 (t80) outliers start: 20 outliers final: 17 residues processed: 77 average time/residue: 0.1885 time to fit residues: 17.2471 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 : 0.330 ------------------------------------------------------------------------------- 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 82 ASP Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 106 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 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 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 81 GLN C 83 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.144425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125893 restraints weight = 6641.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.128796 restraints weight = 4004.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.130642 restraints weight = 2812.696| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.5440 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= 0.165 Angle : 0.741 13.498 4381 Z= 0.379 Chirality : 0.046 0.216 482 Planarity : 0.005 0.060 566 Dihedral : 4.949 42.176 458 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 6.92 % Allowed : 22.64 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.36 (0.41), residues: 414 helix: -0.29 (1.37), residues: 15 sheet: -0.06 (0.43), residues: 145 loop : -1.51 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.018 0.002 PHE B 392 TYR 0.013 0.001 TYR A 49 ARG 0.002 0.000 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 102) hydrogen bonds : angle 5.61718 ( 252) SS BOND : bond 0.00786 ( 6) SS BOND : angle 2.01746 ( 12) covalent geometry : bond 0.00401 ( 3204) covalent geometry : angle 0.73455 ( 4369) *********************** 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 79 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8666 (mp) cc_final: 0.8185 (mt) REVERT: C 3 GLN cc_start: 0.7864 (pp30) cc_final: 0.7438 (pp30) REVERT: C 59 TYR cc_start: 0.7992 (m-80) cc_final: 0.7274 (m-80) REVERT: B 351 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.6970 (t80) outliers start: 22 outliers final: 19 residues processed: 73 average time/residue: 0.1848 time to fit residues: 16.2309 Evaluate side-chains 75 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 A residue 106 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 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 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 434 ILE 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 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.144717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.126434 restraints weight = 6528.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.129311 restraints weight = 3911.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.131281 restraints weight = 2742.382| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.5537 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= 0.157 Angle : 0.745 13.587 4381 Z= 0.381 Chirality : 0.045 0.215 482 Planarity : 0.005 0.056 566 Dihedral : 4.925 41.697 458 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 6.60 % Allowed : 22.33 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.37 (0.41), residues: 414 helix: -0.42 (1.35), residues: 15 sheet: -0.14 (0.42), residues: 155 loop : -1.50 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.021 0.002 PHE B 392 TYR 0.012 0.001 TYR A 49 ARG 0.003 0.000 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 102) hydrogen bonds : angle 5.57705 ( 252) SS BOND : bond 0.00792 ( 6) SS BOND : angle 1.99307 ( 12) covalent geometry : bond 0.00383 ( 3204) covalent geometry : angle 0.73870 ( 4369) ********************** 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: 21 poor density : 53 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8631 (mp) cc_final: 0.8176 (mt) REVERT: A 11 LEU cc_start: 0.8122 (mt) cc_final: 0.7797 (mp) REVERT: C 3 GLN cc_start: 0.7850 (pp30) cc_final: 0.7426 (pp30) REVERT: C 59 TYR cc_start: 0.8007 (m-80) cc_final: 0.7265 (m-80) REVERT: B 351 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.6946 (t80) REVERT: B 455 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7998 (tt) outliers start: 21 outliers final: 18 residues processed: 69 average time/residue: 0.1597 time to fit residues: 13.2108 Evaluate side-chains 74 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 106 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 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 455 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.6314 > 50: distance: 14 - 145: 3.003 distance: 20 - 144: 12.597 distance: 21 - 138: 23.878 distance: 24 - 135: 14.981 distance: 67 - 71: 20.037 distance: 71 - 72: 21.079 distance: 72 - 73: 28.133 distance: 72 - 75: 15.140 distance: 73 - 74: 13.376 distance: 73 - 83: 20.799 distance: 75 - 76: 53.085 distance: 76 - 77: 10.031 distance: 76 - 78: 24.522 distance: 77 - 79: 38.299 distance: 78 - 80: 27.984 distance: 79 - 81: 14.508 distance: 80 - 81: 9.402 distance: 81 - 82: 23.899 distance: 83 - 84: 13.432 distance: 84 - 85: 14.548 distance: 84 - 87: 36.462 distance: 85 - 86: 18.693 distance: 85 - 92: 9.849 distance: 87 - 88: 23.375 distance: 88 - 89: 9.504 distance: 89 - 90: 7.283 distance: 90 - 91: 15.613 distance: 92 - 93: 3.284 distance: 93 - 94: 24.452 distance: 93 - 96: 44.881 distance: 94 - 95: 22.232 distance: 94 - 100: 18.079 distance: 96 - 97: 42.648 distance: 97 - 98: 26.964 distance: 97 - 99: 13.174 distance: 100 - 101: 11.317 distance: 100 - 106: 17.205 distance: 101 - 102: 19.816 distance: 101 - 104: 16.078 distance: 102 - 103: 25.889 distance: 102 - 107: 11.427 distance: 104 - 105: 19.500 distance: 105 - 106: 12.384 distance: 107 - 108: 21.974 distance: 108 - 109: 5.767 distance: 109 - 110: 21.353 distance: 109 - 112: 7.409 distance: 112 - 113: 6.800 distance: 113 - 114: 13.675 distance: 113 - 116: 11.566 distance: 114 - 115: 30.909 distance: 114 - 117: 23.531 distance: 117 - 118: 20.390 distance: 118 - 119: 11.721 distance: 118 - 121: 42.971 distance: 119 - 120: 17.097 distance: 119 - 128: 13.688 distance: 121 - 122: 11.032 distance: 122 - 123: 29.058 distance: 122 - 124: 35.734 distance: 123 - 125: 34.130 distance: 124 - 126: 14.192 distance: 125 - 127: 30.835 distance: 126 - 127: 14.645 distance: 128 - 129: 17.924 distance: 129 - 130: 20.767 distance: 129 - 132: 14.466 distance: 130 - 131: 10.835 distance: 130 - 135: 24.399 distance: 132 - 133: 22.425 distance: 132 - 134: 20.527 distance: 135 - 136: 28.974 distance: 136 - 137: 23.732 distance: 137 - 138: 19.929 distance: 137 - 139: 12.558 distance: 139 - 140: 21.120 distance: 140 - 141: 12.080 distance: 140 - 143: 22.096 distance: 141 - 142: 15.356 distance: 141 - 145: 12.473 distance: 142 - 187: 18.639 distance: 143 - 144: 22.478