Starting phenix.real_space_refine on Fri Dec 27 06:16:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvh_34127/12_2024/7yvh_34127.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvh_34127/12_2024/7yvh_34127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvh_34127/12_2024/7yvh_34127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvh_34127/12_2024/7yvh_34127.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvh_34127/12_2024/7yvh_34127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvh_34127/12_2024/7yvh_34127.cif" } resolution = 3.6 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= -0.000 sd= 0.027 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 1988 2.51 5 N 530 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3124 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 818 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 865 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: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1441 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 83 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': 3} Unresolved non-hydrogen planarities: 75 Time building chain proxies: 4.41, per 1000 atoms: 1.41 Number of scatterers: 3124 At special positions: 0 Unit cell: (60.68, 70.52, 100.86, 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 590 8.00 N 530 7.00 C 1988 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=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 395.8 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: 762 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 6 sheets defined 9.5% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.074A 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: 4.152A 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: 4.910A 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: 3.817A 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: 6.579A pdb=" N LEU A 11 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 84 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.586A 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 removed outlier: 3.708A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.827A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.589A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 97 hydrogen bonds defined for protein. 243 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: 0.79 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 500 1.30 - 1.43: 919 1.43 - 1.56: 1763 1.56 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 3202 Sorted by residual: bond pdb=" CA ARG C 97 " pdb=" C ARG C 97 " ideal model delta sigma weight residual 1.523 1.430 0.094 1.21e-02 6.83e+03 5.98e+01 bond pdb=" C ARG C 97 " pdb=" O ARG C 97 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.14e-02 7.69e+03 3.35e+01 bond pdb=" CB TYR B 473 " pdb=" CG TYR B 473 " ideal model delta sigma weight residual 1.512 1.421 0.091 2.20e-02 2.07e+03 1.70e+01 bond pdb=" CB TYR A 98 " pdb=" CG TYR A 98 " ideal model delta sigma weight residual 1.512 1.425 0.087 2.20e-02 2.07e+03 1.56e+01 bond pdb=" CA TYR A 98 " pdb=" CB TYR A 98 " ideal model delta sigma weight residual 1.533 1.473 0.060 1.72e-02 3.38e+03 1.22e+01 ... (remaining 3197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 4292 3.53 - 7.05: 61 7.05 - 10.58: 10 10.58 - 14.11: 0 14.11 - 17.63: 2 Bond angle restraints: 4365 Sorted by residual: angle pdb=" N GLN B 474 " pdb=" CA GLN B 474 " pdb=" C GLN B 474 " ideal model delta sigma weight residual 108.86 125.29 -16.43 1.41e+00 5.03e-01 1.36e+02 angle pdb=" C TYR A 98 " pdb=" CA TYR A 98 " pdb=" CB TYR A 98 " ideal model delta sigma weight residual 110.43 92.80 17.63 1.68e+00 3.54e-01 1.10e+02 angle pdb=" O ILE B 472 " pdb=" C ILE B 472 " pdb=" N TYR B 473 " ideal model delta sigma weight residual 122.99 117.70 5.29 1.07e+00 8.73e-01 2.45e+01 angle pdb=" O TYR A 98 " pdb=" C TYR A 98 " pdb=" N THR A 99 " ideal model delta sigma weight residual 123.46 118.79 4.67 9.90e-01 1.02e+00 2.23e+01 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 124.75 -10.35 2.30e+00 1.89e-01 2.03e+01 ... (remaining 4360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.23: 1763 23.23 - 46.46: 93 46.46 - 69.69: 13 69.69 - 92.92: 1 92.92 - 116.15: 1 Dihedral angle restraints: 1871 sinusoidal: 667 harmonic: 1204 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 -63.85 -116.15 0 5.00e+00 4.00e-02 5.40e+02 dihedral pdb=" C TYR A 98 " pdb=" N TYR A 98 " pdb=" CA TYR A 98 " pdb=" CB TYR A 98 " ideal model delta harmonic sigma weight residual -122.60 -101.20 -21.40 0 2.50e+00 1.60e-01 7.33e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 48.05 44.95 1 1.00e+01 1.00e-02 2.81e+01 ... (remaining 1868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 432 0.094 - 0.187: 40 0.187 - 0.280: 6 0.280 - 0.374: 1 0.374 - 0.467: 1 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA GLN B 474 " pdb=" N GLN B 474 " pdb=" C GLN B 474 " pdb=" CB GLN B 474 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+00 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 2.14 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CB THR C 112 " pdb=" CA THR C 112 " pdb=" OG1 THR C 112 " pdb=" CG2 THR C 112 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 477 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 94 " -0.035 2.00e-02 2.50e+03 2.57e-02 1.65e+01 pdb=" CG TRP A 94 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP A 94 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 94 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 94 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 94 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 94 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 94 " 0.062 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO A 95 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 98 " 0.006 2.00e-02 2.50e+03 1.83e-02 6.68e+00 pdb=" CG TYR A 98 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 98 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 98 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 98 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 98 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 98 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 98 " -0.012 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 22 2.53 - 3.12: 2487 3.12 - 3.72: 4482 3.72 - 4.31: 6260 4.31 - 4.90: 10416 Nonbonded interactions: 23667 Sorted by model distance: nonbonded pdb=" CD ARG B 403 " pdb=" OD1 ASN B 405 " model vdw 1.941 3.440 nonbonded pdb=" O ARG C 31 " pdb=" OH TYR B 473 " model vdw 2.117 3.040 nonbonded pdb=" OG SER C 56 " pdb=" OG1 THR B 415 " model vdw 2.271 3.040 nonbonded pdb=" NZ LYS B 378 " pdb=" O CYS B 379 " model vdw 2.291 3.120 nonbonded pdb=" O TRP A 94 " pdb=" N GLY A 97 " model vdw 2.322 3.120 ... (remaining 23662 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: 5.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.730 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 3202 Z= 0.437 Angle : 1.109 17.632 4365 Z= 0.649 Chirality : 0.063 0.467 480 Planarity : 0.006 0.092 566 Dihedral : 13.300 116.151 1091 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.70 % Favored : 90.82 % Rotamer: Outliers : 1.58 % Allowed : 6.94 % Favored : 91.48 % Cbeta Deviations : 0.52 % 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: -4.17 (0.34), residues: 414 helix: -4.90 (0.26), residues: 21 sheet: -1.77 (0.40), residues: 128 loop : -3.30 (0.31), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.005 TRP A 94 HIS 0.002 0.001 HIS B 505 PHE 0.019 0.002 PHE B 371 TYR 0.041 0.003 TYR A 98 ARG 0.007 0.001 ARG A 61 *********************** 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 114 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.7548 (mp) cc_final: 0.7306 (mp) REVERT: A 79 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7337 (mt0) REVERT: C 6 GLU cc_start: 0.8464 (mp0) cc_final: 0.8178 (mp0) REVERT: C 59 TYR cc_start: 0.8453 (m-80) cc_final: 0.8251 (m-80) outliers start: 5 outliers final: 2 residues processed: 113 average time/residue: 0.1830 time to fit residues: 24.0226 Evaluate side-chains 64 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.0870 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3202 Z= 0.230 Angle : 0.789 18.902 4365 Z= 0.401 Chirality : 0.050 0.329 480 Planarity : 0.006 0.086 566 Dihedral : 5.225 52.192 463 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.38 % Favored : 96.14 % Rotamer: Outliers : 4.10 % Allowed : 16.40 % Favored : 79.50 % 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: -2.58 (0.37), residues: 414 helix: -3.58 (0.68), residues: 23 sheet: -0.70 (0.44), residues: 122 loop : -2.15 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 47 HIS 0.002 0.001 HIS B 519 PHE 0.011 0.001 PHE B 371 TYR 0.017 0.002 TYR A 49 ARG 0.005 0.001 ARG A 45 *********************** 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 84 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.278 Fit side-chains REVERT: C 46 GLU cc_start: 0.7555 (pt0) cc_final: 0.7271 (tt0) REVERT: B 390 LEU cc_start: 0.7824 (mt) cc_final: 0.7476 (mt) REVERT: B 474 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6540 (pp30) outliers start: 13 outliers final: 10 residues processed: 78 average time/residue: 0.1584 time to fit residues: 14.8863 Evaluate side-chains 67 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 0.0670 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 0.0010 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 0.0970 overall best weight: 0.2322 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3202 Z= 0.175 Angle : 0.730 18.697 4365 Z= 0.368 Chirality : 0.047 0.308 480 Planarity : 0.005 0.071 566 Dihedral : 4.823 44.539 460 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.42 % Allowed : 21.14 % Favored : 74.45 % 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: -1.98 (0.39), residues: 414 helix: -2.62 (0.91), residues: 23 sheet: -0.29 (0.46), residues: 119 loop : -1.77 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 94 HIS 0.002 0.001 HIS B 519 PHE 0.016 0.001 PHE B 371 TYR 0.020 0.002 TYR C 59 ARG 0.004 0.000 ARG A 24 *********************** 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 87 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7532 (pt0) cc_final: 0.7279 (tt0) REVERT: B 386 LYS cc_start: 0.9091 (tptt) cc_final: 0.8580 (tppt) REVERT: B 390 LEU cc_start: 0.7732 (mt) cc_final: 0.7018 (mt) REVERT: B 474 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6618 (pp30) outliers start: 14 outliers final: 8 residues processed: 80 average time/residue: 0.1476 time to fit residues: 14.4511 Evaluate side-chains 69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3202 Z= 0.204 Angle : 0.709 18.677 4365 Z= 0.360 Chirality : 0.046 0.242 480 Planarity : 0.005 0.061 566 Dihedral : 4.804 46.570 459 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.99 % Allowed : 23.03 % Favored : 70.98 % 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: -1.65 (0.40), residues: 414 helix: -2.19 (0.96), residues: 23 sheet: -0.03 (0.46), residues: 123 loop : -1.59 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 94 HIS 0.001 0.000 HIS B 519 PHE 0.015 0.002 PHE B 371 TYR 0.010 0.001 TYR A 91 ARG 0.003 0.000 ARG A 24 *********************** 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 90 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.356 Fit side-chains REVERT: A 18 ARG cc_start: 0.8068 (mtp-110) cc_final: 0.7585 (mtp-110) REVERT: B 356 LYS cc_start: 0.8284 (mmmt) cc_final: 0.8069 (tptp) REVERT: B 386 LYS cc_start: 0.9025 (tptt) cc_final: 0.8491 (tppt) REVERT: B 390 LEU cc_start: 0.7723 (mt) cc_final: 0.6942 (mt) REVERT: B 474 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7229 (pp30) outliers start: 19 outliers final: 14 residues processed: 83 average time/residue: 0.1662 time to fit residues: 16.5237 Evaluate side-chains 77 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 32 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3202 Z= 0.197 Angle : 0.823 25.699 4365 Z= 0.414 Chirality : 0.050 0.396 480 Planarity : 0.005 0.063 566 Dihedral : 4.910 48.664 459 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.36 % Allowed : 24.92 % Favored : 69.72 % 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: -1.50 (0.40), residues: 414 helix: -2.01 (0.96), residues: 23 sheet: 0.08 (0.46), residues: 125 loop : -1.52 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 94 HIS 0.001 0.001 HIS B 505 PHE 0.013 0.001 PHE A 71 TYR 0.009 0.001 TYR A 91 ARG 0.004 0.000 ARG A 18 *********************** 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 83 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: B 356 LYS cc_start: 0.8256 (mmmt) cc_final: 0.8018 (tptp) REVERT: B 386 LYS cc_start: 0.9028 (tptt) cc_final: 0.8769 (tppt) REVERT: B 390 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7532 (mt) REVERT: B 474 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7529 (pp30) outliers start: 17 outliers final: 13 residues processed: 75 average time/residue: 0.1608 time to fit residues: 14.6849 Evaluate side-chains 74 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3202 Z= 0.192 Angle : 0.810 25.339 4365 Z= 0.407 Chirality : 0.050 0.384 480 Planarity : 0.005 0.064 566 Dihedral : 4.940 48.924 459 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.68 % Allowed : 25.87 % Favored : 68.45 % 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: -1.47 (0.40), residues: 414 helix: -1.76 (1.01), residues: 23 sheet: 0.22 (0.46), residues: 123 loop : -1.57 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 94 HIS 0.001 0.000 HIS B 519 PHE 0.013 0.001 PHE A 71 TYR 0.021 0.001 TYR C 79 ARG 0.002 0.000 ARG A 24 *********************** 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 83 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.368 Fit side-chains REVERT: B 356 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7996 (tptp) REVERT: B 375 PHE cc_start: 0.6364 (m-80) cc_final: 0.6145 (m-80) REVERT: B 474 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7656 (pp30) outliers start: 18 outliers final: 15 residues processed: 74 average time/residue: 0.1670 time to fit residues: 14.8088 Evaluate side-chains 76 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3202 Z= 0.220 Angle : 0.794 23.420 4365 Z= 0.402 Chirality : 0.049 0.326 480 Planarity : 0.005 0.062 566 Dihedral : 5.010 48.873 459 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 6.94 % Allowed : 24.61 % Favored : 68.45 % 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: -1.41 (0.40), residues: 414 helix: -1.87 (0.98), residues: 23 sheet: 0.27 (0.46), residues: 122 loop : -1.51 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 94 HIS 0.001 0.000 HIS B 519 PHE 0.016 0.001 PHE A 71 TYR 0.009 0.001 TYR B 489 ARG 0.003 0.000 ARG A 61 *********************** 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 82 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 356 LYS cc_start: 0.8219 (mmmt) cc_final: 0.8010 (tptp) REVERT: B 386 LYS cc_start: 0.8951 (tptp) cc_final: 0.8621 (tppt) REVERT: B 474 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7661 (pp30) outliers start: 22 outliers final: 17 residues processed: 72 average time/residue: 0.1644 time to fit residues: 14.3500 Evaluate side-chains 76 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 0.0670 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3202 Z= 0.233 Angle : 0.832 25.104 4365 Z= 0.418 Chirality : 0.050 0.380 480 Planarity : 0.005 0.061 566 Dihedral : 5.107 49.325 459 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 6.31 % Allowed : 24.29 % Favored : 69.40 % 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: -1.96 (0.98), residues: 23 sheet: 0.19 (0.46), residues: 125 loop : -1.44 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 94 HIS 0.001 0.000 HIS B 519 PHE 0.028 0.002 PHE A 71 TYR 0.015 0.002 TYR A 49 ARG 0.002 0.000 ARG A 61 *********************** 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 76 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7799 (pp30) outliers start: 20 outliers final: 16 residues processed: 68 average time/residue: 0.1732 time to fit residues: 14.1718 Evaluate side-chains 70 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3202 Z= 0.211 Angle : 0.809 24.845 4365 Z= 0.406 Chirality : 0.050 0.364 480 Planarity : 0.005 0.059 566 Dihedral : 4.993 47.594 459 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 6.31 % Allowed : 24.29 % Favored : 69.40 % 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: -1.32 (0.41), residues: 414 helix: -1.86 (1.03), residues: 23 sheet: 0.26 (0.47), residues: 125 loop : -1.43 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 35 HIS 0.011 0.004 HIS B 519 PHE 0.024 0.001 PHE A 71 TYR 0.016 0.001 TYR B 380 ARG 0.002 0.000 ARG A 18 *********************** 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 76 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLN cc_start: 0.7975 (mp10) cc_final: 0.7653 (mt0) REVERT: B 371 PHE cc_start: 0.5067 (OUTLIER) cc_final: 0.4065 (t80) REVERT: B 474 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7847 (pp30) outliers start: 20 outliers final: 16 residues processed: 67 average time/residue: 0.1690 time to fit residues: 13.6529 Evaluate side-chains 74 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3202 Z= 0.262 Angle : 0.833 24.159 4365 Z= 0.420 Chirality : 0.051 0.362 480 Planarity : 0.005 0.063 566 Dihedral : 5.208 49.745 459 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.68 % Allowed : 24.92 % Favored : 69.40 % 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: -2.00 (0.99), residues: 23 sheet: 0.15 (0.45), residues: 135 loop : -1.46 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 35 HIS 0.007 0.002 HIS B 519 PHE 0.021 0.002 PHE A 71 TYR 0.015 0.002 TYR A 49 ARG 0.004 0.001 ARG A 18 ********************** 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 73 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLN cc_start: 0.7931 (mp10) cc_final: 0.7555 (mp10) REVERT: B 371 PHE cc_start: 0.5101 (OUTLIER) cc_final: 0.4078 (t80) REVERT: B 474 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7839 (pp30) outliers start: 18 outliers final: 14 residues processed: 67 average time/residue: 0.1914 time to fit residues: 15.4619 Evaluate side-chains 69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 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 = 0.3787 r_free = 0.3787 target = 0.115956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095437 restraints weight = 8042.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.098093 restraints weight = 4338.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.099864 restraints weight = 2923.829| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3202 Z= 0.214 Angle : 0.820 24.164 4365 Z= 0.414 Chirality : 0.051 0.359 480 Planarity : 0.005 0.060 566 Dihedral : 5.085 47.625 459 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.36 % Allowed : 24.92 % Favored : 69.72 % 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: -1.26 (0.41), residues: 414 helix: -1.90 (1.03), residues: 23 sheet: 0.28 (0.48), residues: 125 loop : -1.36 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 94 HIS 0.001 0.000 HIS B 519 PHE 0.019 0.001 PHE A 71 TYR 0.019 0.002 TYR C 107 ARG 0.003 0.000 ARG A 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.50 seconds wall clock time: 28 minutes 31.46 seconds (1711.46 seconds total)