Starting phenix.real_space_refine on Fri Dec 27 05:55:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7k_33668/12_2024/7y7k_33668.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7k_33668/12_2024/7y7k_33668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y7k_33668/12_2024/7y7k_33668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7k_33668/12_2024/7y7k_33668.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7k_33668/12_2024/7y7k_33668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7k_33668/12_2024/7y7k_33668.cif" } resolution = 4.4 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= -0.003 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 1832 2.51 5 N 505 2.21 5 O 594 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-5532/modules/chem_data/mon_lib" Total number of atoms: 2942 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1230 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 9, 'TRANS': 169} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 157 Chain: "B" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 953 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 759 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 103} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 3.89, per 1000 atoms: 1.32 Number of scatterers: 2942 At special positions: 0 Unit cell: (56.58, 64.78, 104.14, 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 11 16.00 O 594 8.00 N 505 7.00 C 1832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.01 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " 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: 0.80 Conformation dependent library (CDL) restraints added in 457.5 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 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: 9 helices and 6 sheets defined 11.8% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.118A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.651A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'C' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.693A pdb=" N PHE B 80 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.127A pdb=" N TRP B 36 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER B 52 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TRP B 38 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 50 removed outlier: 6.235A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASP C 34 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR C 93 " --> pdb=" O ASP C 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 50 removed outlier: 6.235A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASP C 34 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR C 93 " --> pdb=" O ASP C 34 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 264 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: 0.65 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 494 1.28 - 1.42: 781 1.42 - 1.55: 1715 1.55 - 1.68: 3 1.68 - 1.81: 11 Bond restraints: 3004 Sorted by residual: bond pdb=" C ASN A 439 " pdb=" O ASN A 439 " ideal model delta sigma weight residual 1.236 1.151 0.085 1.18e-02 7.18e+03 5.20e+01 bond pdb=" C ARG B 102 " pdb=" N SER B 103 " ideal model delta sigma weight residual 1.332 1.288 0.045 1.40e-02 5.10e+03 1.01e+01 bond pdb=" C ASN A 439 " pdb=" N ASN A 440 " ideal model delta sigma weight residual 1.334 1.291 0.044 1.38e-02 5.25e+03 1.01e+01 bond pdb=" C LYS A 424 " pdb=" N LEU A 425 " ideal model delta sigma weight residual 1.335 1.265 0.070 3.04e-02 1.08e+03 5.32e+00 bond pdb=" CA GLU B 1 " pdb=" C GLU B 1 " ideal model delta sigma weight residual 1.525 1.481 0.044 2.10e-02 2.27e+03 4.49e+00 ... (remaining 2999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 3702 2.41 - 4.81: 306 4.81 - 7.22: 78 7.22 - 9.62: 21 9.62 - 12.03: 5 Bond angle restraints: 4112 Sorted by residual: angle pdb=" N TYR A 489 " pdb=" CA TYR A 489 " pdb=" C TYR A 489 " ideal model delta sigma weight residual 109.65 119.96 -10.31 1.56e+00 4.11e-01 4.37e+01 angle pdb=" N THR A 478 " pdb=" CA THR A 478 " pdb=" C THR A 478 " ideal model delta sigma weight residual 109.06 119.62 -10.56 1.78e+00 3.16e-01 3.52e+01 angle pdb=" N TYR B 105 " pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 110.80 98.77 12.03 2.13e+00 2.20e-01 3.19e+01 angle pdb=" O ARG B 102 " pdb=" C ARG B 102 " pdb=" N SER B 103 " ideal model delta sigma weight residual 122.59 115.43 7.16 1.33e+00 5.65e-01 2.89e+01 angle pdb=" N PHE A 464 " pdb=" CA PHE A 464 " pdb=" C PHE A 464 " ideal model delta sigma weight residual 110.80 121.21 -10.41 2.13e+00 2.20e-01 2.39e+01 ... (remaining 4107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 1649 17.46 - 34.93: 87 34.93 - 52.39: 20 52.39 - 69.86: 9 69.86 - 87.32: 4 Dihedral angle restraints: 1769 sinusoidal: 564 harmonic: 1205 Sorted by residual: dihedral pdb=" CA GLN C 1 " pdb=" C GLN C 1 " pdb=" N SER C 2 " pdb=" CA SER C 2 " ideal model delta harmonic sigma weight residual -180.00 -161.81 -18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ALA C 86 " pdb=" C ALA C 86 " pdb=" N ASP C 87 " pdb=" CA ASP C 87 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN C 53 " pdb=" C ASN C 53 " pdb=" N ASN C 54 " pdb=" CA ASN C 54 " ideal model delta harmonic sigma weight residual 180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 1766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 285 0.056 - 0.112: 129 0.112 - 0.167: 42 0.167 - 0.223: 9 0.223 - 0.279: 7 Chirality restraints: 472 Sorted by residual: chirality pdb=" CA TYR A 489 " pdb=" N TYR A 489 " pdb=" C TYR A 489 " pdb=" CB TYR A 489 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA PRO A 479 " pdb=" N PRO A 479 " pdb=" C PRO A 479 " pdb=" CB PRO A 479 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB VAL A 362 " pdb=" CA VAL A 362 " pdb=" CG1 VAL A 362 " pdb=" CG2 VAL A 362 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 469 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 439 " -0.023 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C ASN A 439 " 0.081 2.00e-02 2.50e+03 pdb=" O ASN A 439 " -0.031 2.00e-02 2.50e+03 pdb=" N ASN A 440 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO A 491 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 38 " 0.024 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR C 38 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR C 38 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR C 38 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR C 38 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR C 38 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR C 38 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 38 " -0.014 2.00e-02 2.50e+03 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 568 2.75 - 3.29: 2907 3.29 - 3.83: 4888 3.83 - 4.36: 5365 4.36 - 4.90: 9159 Nonbonded interactions: 22887 Sorted by model distance: nonbonded pdb=" OG SER C 27 " pdb=" N THR C 96 " model vdw 2.215 3.120 nonbonded pdb=" O THR C 5 " pdb=" N THR C 23 " model vdw 2.251 3.120 nonbonded pdb=" O THR A 345 " pdb=" NH2 ARG A 509 " model vdw 2.253 3.120 nonbonded pdb=" NE2 GLN B 41 " pdb=" O LYS B 45 " model vdw 2.266 3.120 nonbonded pdb=" O CYS C 90 " pdb=" N GLY C 103 " model vdw 2.269 3.120 ... (remaining 22882 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: 3.960 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.780 Find NCS groups from input model: 0.020 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 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 : 0.010 0.104 3004 Z= 0.662 Angle : 1.632 12.028 4112 Z= 0.938 Chirality : 0.074 0.279 472 Planarity : 0.010 0.116 540 Dihedral : 13.106 87.323 992 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 33.93 Ramachandran Plot: Outliers : 3.61 % Allowed : 10.34 % Favored : 86.06 % Rotamer: Outliers : 3.90 % Allowed : 7.09 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.38), residues: 416 helix: -3.92 (0.53), residues: 36 sheet: 0.24 (0.48), residues: 126 loop : -2.47 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 49 HIS 0.007 0.002 HIS C 33 PHE 0.024 0.003 PHE A 456 TYR 0.069 0.006 TYR C 38 ARG 0.027 0.003 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 TYR cc_start: 0.7862 (m-80) cc_final: 0.7483 (m-80) REVERT: C 16 GLN cc_start: 0.6542 (OUTLIER) cc_final: 0.5606 (pp30) REVERT: C 41 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8184 (tt) outliers start: 11 outliers final: 2 residues processed: 71 average time/residue: 0.2322 time to fit residues: 18.7354 Evaluate side-chains 29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN C 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3004 Z= 0.230 Angle : 0.794 7.863 4112 Z= 0.418 Chirality : 0.050 0.227 472 Planarity : 0.005 0.034 540 Dihedral : 5.565 19.446 454 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.96 % Allowed : 7.45 % Favored : 91.59 % Rotamer: Outliers : 0.71 % Allowed : 2.48 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.39), residues: 416 helix: -4.56 (0.37), residues: 24 sheet: 0.09 (0.45), residues: 135 loop : -1.73 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS B 100 PHE 0.011 0.002 PHE A 456 TYR 0.029 0.002 TYR C 38 ARG 0.004 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 TYR cc_start: 0.7986 (m-80) cc_final: 0.7727 (m-80) REVERT: B 107 TYR cc_start: 0.6022 (p90) cc_final: 0.5747 (p90) REVERT: C 41 LEU cc_start: 0.8568 (tp) cc_final: 0.8347 (tt) outliers start: 2 outliers final: 0 residues processed: 41 average time/residue: 0.3017 time to fit residues: 13.9188 Evaluate side-chains 23 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 3004 Z= 0.494 Angle : 1.010 8.463 4112 Z= 0.537 Chirality : 0.054 0.275 472 Planarity : 0.006 0.043 540 Dihedral : 7.198 22.032 454 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 25.99 Ramachandran Plot: Outliers : 0.96 % Allowed : 11.54 % Favored : 87.50 % Rotamer: Outliers : 0.35 % Allowed : 3.55 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.39), residues: 416 helix: -3.06 (0.67), residues: 25 sheet: 0.07 (0.44), residues: 123 loop : -1.80 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 49 HIS 0.004 0.001 HIS B 100 PHE 0.019 0.002 PHE A 374 TYR 0.028 0.003 TYR C 38 ARG 0.010 0.002 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 GLU cc_start: 0.6810 (tt0) cc_final: 0.6210 (mt-10) outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.2175 time to fit residues: 7.3642 Evaluate side-chains 15 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3004 Z= 0.329 Angle : 0.838 8.984 4112 Z= 0.441 Chirality : 0.050 0.328 472 Planarity : 0.005 0.046 540 Dihedral : 6.350 23.566 454 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.21 % Favored : 92.07 % Rotamer: Outliers : 0.35 % Allowed : 2.48 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.39), residues: 416 helix: -2.44 (0.84), residues: 25 sheet: 0.22 (0.46), residues: 124 loop : -1.87 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 353 HIS 0.006 0.002 HIS B 100 PHE 0.013 0.002 PHE A 374 TYR 0.019 0.002 TYR C 38 ARG 0.007 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 513 LEU cc_start: 0.8622 (pp) cc_final: 0.8402 (mp) REVERT: B 6 GLU cc_start: 0.6236 (tt0) cc_final: 0.5799 (tt0) REVERT: C 40 GLN cc_start: 0.8739 (pt0) cc_final: 0.8236 (pm20) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.1764 time to fit residues: 4.8307 Evaluate side-chains 17 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3004 Z= 0.219 Angle : 0.691 8.400 4112 Z= 0.361 Chirality : 0.047 0.312 472 Planarity : 0.004 0.051 540 Dihedral : 5.584 20.696 454 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.62 % Favored : 89.66 % Rotamer: Outliers : 0.35 % Allowed : 1.77 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.40), residues: 416 helix: -2.31 (0.91), residues: 25 sheet: 0.32 (0.45), residues: 124 loop : -1.79 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.002 0.001 HIS B 100 PHE 0.007 0.001 PHE C 102 TYR 0.024 0.002 TYR C 100 ARG 0.004 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 ASN cc_start: 0.6119 (OUTLIER) cc_final: 0.5429 (m110) REVERT: B 95 TYR cc_start: 0.8107 (m-80) cc_final: 0.7782 (m-80) REVERT: C 40 GLN cc_start: 0.8712 (pt0) cc_final: 0.8220 (pm20) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.2056 time to fit residues: 7.1291 Evaluate side-chains 20 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.6552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3004 Z= 0.201 Angle : 0.639 6.826 4112 Z= 0.332 Chirality : 0.046 0.169 472 Planarity : 0.004 0.052 540 Dihedral : 5.251 20.026 454 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.93 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.41), residues: 416 helix: -2.11 (0.94), residues: 25 sheet: 0.22 (0.44), residues: 129 loop : -1.81 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 122 HIS 0.002 0.001 HIS B 100 PHE 0.022 0.002 PHE A 486 TYR 0.021 0.002 TYR C 100 ARG 0.004 0.001 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 GLU cc_start: 0.6167 (tt0) cc_final: 0.5288 (pt0) REVERT: B 20 LEU cc_start: 0.8123 (pp) cc_final: 0.7730 (mm) REVERT: C 40 GLN cc_start: 0.8701 (pt0) cc_final: 0.8222 (pm20) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.2077 time to fit residues: 7.6971 Evaluate side-chains 20 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.0040 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3004 Z= 0.216 Angle : 0.696 9.495 4112 Z= 0.357 Chirality : 0.049 0.344 472 Planarity : 0.004 0.053 540 Dihedral : 5.311 19.858 454 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.41 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.40), residues: 416 helix: -2.76 (0.81), residues: 31 sheet: 0.20 (0.44), residues: 129 loop : -1.96 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS B 100 PHE 0.019 0.002 PHE A 486 TYR 0.020 0.002 TYR C 100 ARG 0.003 0.001 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 GLN cc_start: 0.8688 (pt0) cc_final: 0.8245 (pm20) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1564 time to fit residues: 4.8088 Evaluate side-chains 20 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.7134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3004 Z= 0.148 Angle : 0.616 7.623 4112 Z= 0.312 Chirality : 0.047 0.226 472 Planarity : 0.004 0.054 540 Dihedral : 4.623 18.093 454 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.45 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.41), residues: 416 helix: -2.65 (0.82), residues: 31 sheet: 0.42 (0.45), residues: 129 loop : -1.91 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 436 HIS 0.001 0.001 HIS B 100 PHE 0.013 0.001 PHE A 486 TYR 0.018 0.001 TYR C 100 ARG 0.002 0.000 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 LEU cc_start: 0.7845 (pp) cc_final: 0.7326 (mm) REVERT: B 120 ASP cc_start: 0.8040 (p0) cc_final: 0.7541 (m-30) REVERT: C 40 GLN cc_start: 0.8649 (pt0) cc_final: 0.8172 (pm20) REVERT: C 41 LEU cc_start: 0.8821 (tp) cc_final: 0.8620 (tt) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1662 time to fit residues: 6.0436 Evaluate side-chains 22 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 27 optimal weight: 0.2980 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.7313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3004 Z= 0.225 Angle : 0.651 7.296 4112 Z= 0.332 Chirality : 0.046 0.205 472 Planarity : 0.004 0.052 540 Dihedral : 5.014 19.216 454 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.38 % Favored : 90.14 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.41), residues: 416 helix: -1.74 (0.98), residues: 25 sheet: 0.19 (0.44), residues: 129 loop : -1.91 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 353 HIS 0.002 0.001 HIS B 100 PHE 0.016 0.002 PHE A 486 TYR 0.017 0.002 TYR C 100 ARG 0.003 0.001 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ASP cc_start: 0.7818 (p0) cc_final: 0.7440 (m-30) REVERT: C 40 GLN cc_start: 0.8734 (pt0) cc_final: 0.8255 (pm20) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1826 time to fit residues: 5.7247 Evaluate side-chains 20 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.7737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3004 Z= 0.241 Angle : 0.673 6.933 4112 Z= 0.347 Chirality : 0.047 0.214 472 Planarity : 0.004 0.054 540 Dihedral : 5.324 20.239 454 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.62 % Favored : 89.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.41), residues: 416 helix: -1.93 (0.85), residues: 31 sheet: -0.36 (0.42), residues: 139 loop : -1.89 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 122 HIS 0.002 0.001 HIS B 100 PHE 0.016 0.002 PHE A 486 TYR 0.018 0.002 TYR B 35 ARG 0.003 0.001 ARG C 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 GLN cc_start: 0.8728 (pt0) cc_final: 0.8250 (pm20) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1654 time to fit residues: 5.1084 Evaluate side-chains 17 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 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 = 0.3582 r_free = 0.3582 target = 0.058078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.050012 restraints weight = 26834.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.051364 restraints weight = 18336.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.052350 restraints weight = 13254.494| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.7777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3004 Z= 0.159 Angle : 0.601 6.126 4112 Z= 0.304 Chirality : 0.046 0.157 472 Planarity : 0.004 0.054 540 Dihedral : 4.706 18.292 454 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.73 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.41), residues: 416 helix: -1.68 (0.92), residues: 31 sheet: -0.12 (0.43), residues: 138 loop : -1.83 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.001 0.001 HIS B 100 PHE 0.014 0.001 PHE A 486 TYR 0.018 0.001 TYR C 100 ARG 0.002 0.001 ARG C 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1256.67 seconds wall clock time: 23 minutes 25.53 seconds (1405.53 seconds total)