Starting phenix.real_space_refine on Sun Mar 10 15:30:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7k_33668/03_2024/7y7k_33668.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7k_33668/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7k_33668/03_2024/7y7k_33668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7k_33668/03_2024/7y7k_33668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7k_33668/03_2024/7y7k_33668.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7k_33668/03_2024/7y7k_33668.pdb" } 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 Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 94": "OD1" <-> "OD2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.14, per 1000 atoms: 0.73 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 - 3.50 Amino acid : False - 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: 1.01 Conformation dependent library (CDL) restraints added in 573.0 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: 0.36 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: 0.75 Time building geometry restraints manager: 1.12 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: 98.77 - 105.84: 95 105.84 - 112.90: 1573 112.90 - 119.97: 1011 119.97 - 127.03: 1402 127.03 - 134.10: 31 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 2.520 nonbonded pdb=" O THR C 5 " pdb=" N THR C 23 " model vdw 2.251 2.520 nonbonded pdb=" O THR A 345 " pdb=" NH2 ARG A 509 " model vdw 2.253 2.520 nonbonded pdb=" NE2 GLN B 41 " pdb=" O LYS B 45 " model vdw 2.266 2.520 nonbonded pdb=" O CYS C 90 " pdb=" N GLY C 103 " model vdw 2.269 2.520 ... (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 ========== 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: 3.890 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: 17.790 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.190 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.070 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.340 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: 0.2211 time to fit residues: 17.8292 Evaluate side-chains 29 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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: 0.6343 moved from start: 0.3842 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= 0.220 Angle : 0.775 7.216 4112 Z= 0.408 Chirality : 0.049 0.209 472 Planarity : 0.004 0.032 540 Dihedral : 5.489 19.463 454 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.96 % Allowed : 7.21 % Favored : 91.83 % Rotamer: Outliers : 0.71 % Allowed : 2.13 % 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: -1.82 (0.39), residues: 416 helix: -4.42 (0.32), residues: 24 sheet: 0.12 (0.46), residues: 129 loop : -1.67 (0.35), residues: 263 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 0.011 0.002 PHE A 456 TYR 0.029 0.002 TYR C 38 ARG 0.005 0.001 ARG B 113 *********************** 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 40 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 TYR cc_start: 0.7979 (m-80) cc_final: 0.7717 (m-80) REVERT: B 107 TYR cc_start: 0.6139 (p90) cc_final: 0.5865 (p90) REVERT: C 41 LEU cc_start: 0.8494 (tp) cc_final: 0.8273 (tt) outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 0.2737 time to fit residues: 12.4032 Evaluate side-chains 22 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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: 0.9990 chunk 11 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3004 Z= 0.250 Angle : 0.700 7.253 4112 Z= 0.370 Chirality : 0.047 0.232 472 Planarity : 0.004 0.038 540 Dihedral : 5.175 19.129 454 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.96 % Allowed : 7.69 % Favored : 91.35 % 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: -1.32 (0.40), residues: 416 helix: -2.31 (0.90), residues: 19 sheet: 0.24 (0.45), residues: 129 loop : -1.41 (0.38), residues: 268 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 0.009 0.001 PHE A 486 TYR 0.023 0.002 TYR C 38 ARG 0.005 0.001 ARG C 26 *********************** 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 35 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8118 (m-80) cc_final: 0.7817 (m-80) REVERT: B 107 TYR cc_start: 0.6244 (p90) cc_final: 0.5945 (p90) REVERT: C 40 GLN cc_start: 0.8354 (pt0) cc_final: 0.7830 (pm20) REVERT: C 41 LEU cc_start: 0.8541 (tp) cc_final: 0.8327 (tt) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.2298 time to fit residues: 9.1233 Evaluate side-chains 21 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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: 0.0020 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.9394 ------------------------------------------------------------------------------- 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 498 GLN ** 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: 0.6636 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 3004 Z= 0.360 Angle : 0.825 9.068 4112 Z= 0.437 Chirality : 0.049 0.272 472 Planarity : 0.005 0.041 540 Dihedral : 6.274 21.199 454 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 28.51 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.17 % Favored : 91.11 % 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: -1.63 (0.40), residues: 416 helix: -1.41 (1.07), residues: 19 sheet: 0.23 (0.47), residues: 123 loop : -1.80 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 49 HIS 0.008 0.003 HIS B 100 PHE 0.016 0.002 PHE A 374 TYR 0.021 0.002 TYR B 35 ARG 0.008 0.002 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 27 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 LEU cc_start: 0.8611 (pp) cc_final: 0.8365 (mp) REVERT: C 40 GLN cc_start: 0.8684 (pt0) cc_final: 0.8164 (pm20) outliers start: 2 outliers final: 0 residues processed: 26 average time/residue: 0.1691 time to fit residues: 5.5546 Evaluate side-chains 15 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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: 0.0870 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 16 optimal weight: 0.0050 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 overall best weight: 0.7174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3004 Z= 0.153 Angle : 0.623 8.493 4112 Z= 0.319 Chirality : 0.046 0.297 472 Planarity : 0.004 0.051 540 Dihedral : 4.729 19.156 454 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.01 % Favored : 93.27 % Rotamer: Outliers : 0.71 % Allowed : 1.06 % Favored : 98.23 % 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: -1.37 (0.41), residues: 416 helix: -0.76 (1.19), residues: 19 sheet: 0.44 (0.48), residues: 125 loop : -1.69 (0.37), residues: 272 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 0.005 0.001 PHE A 490 TYR 0.014 0.001 TYR C 38 ARG 0.003 0.001 ARG B 102 *********************** 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 34 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 ASN cc_start: 0.5609 (OUTLIER) cc_final: 0.4962 (m110) REVERT: B 95 TYR cc_start: 0.8147 (m-80) cc_final: 0.7887 (m-80) REVERT: B 107 TYR cc_start: 0.6080 (p90) cc_final: 0.5780 (p90) REVERT: C 38 TYR cc_start: 0.6981 (m-80) cc_final: 0.6660 (m-10) REVERT: C 40 GLN cc_start: 0.8640 (pt0) cc_final: 0.8122 (pm20) outliers start: 2 outliers final: 0 residues processed: 33 average time/residue: 0.1783 time to fit residues: 7.2414 Evaluate side-chains 22 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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: 0.9980 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3004 Z= 0.173 Angle : 0.645 7.709 4112 Z= 0.330 Chirality : 0.047 0.346 472 Planarity : 0.004 0.050 540 Dihedral : 4.726 18.419 454 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.69 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: -1.28 (0.42), residues: 416 helix: -0.77 (1.20), residues: 19 sheet: 0.42 (0.47), residues: 133 loop : -1.64 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 49 HIS 0.001 0.001 HIS B 100 PHE 0.018 0.001 PHE A 486 TYR 0.013 0.001 TYR C 38 ARG 0.004 0.001 ARG A 509 *********************** 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 26 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8203 (m-80) cc_final: 0.7912 (m-80) REVERT: B 107 TYR cc_start: 0.6125 (p90) cc_final: 0.5781 (p90) REVERT: C 38 TYR cc_start: 0.6969 (m-80) cc_final: 0.6618 (m-10) REVERT: C 40 GLN cc_start: 0.8663 (pt0) cc_final: 0.8332 (pm20) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1971 time to fit residues: 6.2888 Evaluate side-chains 21 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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: 6.9990 chunk 22 optimal weight: 0.0170 chunk 33 optimal weight: 0.0060 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.6368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3004 Z= 0.151 Angle : 0.605 6.456 4112 Z= 0.305 Chirality : 0.045 0.170 472 Planarity : 0.004 0.049 540 Dihedral : 4.473 17.778 454 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.49 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -1.20 (0.42), residues: 416 helix: -0.63 (1.24), residues: 19 sheet: 0.53 (0.47), residues: 133 loop : -1.62 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.002 0.001 HIS C 33 PHE 0.019 0.001 PHE A 486 TYR 0.011 0.001 TYR C 38 ARG 0.006 0.001 ARG B 102 *********************** 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 26 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8182 (m-80) cc_final: 0.7904 (m-80) REVERT: B 107 TYR cc_start: 0.6188 (p90) cc_final: 0.5846 (p90) REVERT: C 38 TYR cc_start: 0.6901 (m-80) cc_final: 0.6615 (m-10) REVERT: C 40 GLN cc_start: 0.8646 (pt0) cc_final: 0.8319 (pm20) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1587 time to fit residues: 5.2667 Evaluate side-chains 22 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 31 optimal weight: 0.1980 chunk 35 optimal weight: 0.0470 chunk 37 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 0.0030 chunk 28 optimal weight: 2.9990 overall best weight: 0.3288 ------------------------------------------------------------------------------- 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: 0.6380 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3004 Z= 0.123 Angle : 0.577 7.143 4112 Z= 0.289 Chirality : 0.046 0.217 472 Planarity : 0.004 0.048 540 Dihedral : 4.000 15.780 454 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.25 % Favored : 93.27 % 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: -1.12 (0.42), residues: 416 helix: -0.68 (1.24), residues: 19 sheet: 0.52 (0.45), residues: 142 loop : -1.59 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS C 33 PHE 0.016 0.001 PHE A 486 TYR 0.011 0.001 TYR C 38 ARG 0.005 0.001 ARG B 102 *********************** 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 28 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8122 (m-80) cc_final: 0.7874 (m-80) REVERT: B 107 TYR cc_start: 0.6104 (p90) cc_final: 0.5705 (p90) REVERT: C 38 TYR cc_start: 0.6789 (m-80) cc_final: 0.6455 (m-10) REVERT: C 40 GLN cc_start: 0.8605 (pt0) cc_final: 0.8280 (pm20) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1529 time to fit residues: 5.4657 Evaluate side-chains 21 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 0.0870 chunk 40 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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: 0.6381 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3004 Z= 0.131 Angle : 0.576 7.550 4112 Z= 0.287 Chirality : 0.045 0.209 472 Planarity : 0.004 0.048 540 Dihedral : 3.915 15.534 454 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.73 % Favored : 92.79 % 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: -1.02 (0.42), residues: 416 helix: -0.47 (1.25), residues: 19 sheet: 0.59 (0.45), residues: 138 loop : -1.50 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.001 0.000 HIS C 33 PHE 0.015 0.001 PHE A 486 TYR 0.011 0.001 TYR C 38 ARG 0.005 0.001 ARG B 102 *********************** 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 27 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8123 (m-80) cc_final: 0.7875 (m-80) REVERT: B 107 TYR cc_start: 0.6218 (p90) cc_final: 0.5771 (p90) REVERT: C 38 TYR cc_start: 0.6817 (m-80) cc_final: 0.6472 (m-10) REVERT: C 40 GLN cc_start: 0.8586 (pt0) cc_final: 0.8269 (pm20) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1895 time to fit residues: 6.3902 Evaluate side-chains 22 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 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: 2.9990 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.0020 chunk 34 optimal weight: 9.9990 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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: 0.6378 moved from start: 0.6843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3004 Z= 0.129 Angle : 0.564 7.671 4112 Z= 0.281 Chirality : 0.045 0.201 472 Planarity : 0.004 0.047 540 Dihedral : 3.934 15.347 454 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.97 % Favored : 92.55 % 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: -1.04 (0.42), residues: 416 helix: -0.47 (1.23), residues: 19 sheet: 0.48 (0.45), residues: 143 loop : -1.48 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS C 33 PHE 0.015 0.001 PHE A 486 TYR 0.011 0.001 TYR C 38 ARG 0.005 0.001 ARG B 102 ********************** 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 26 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: B 95 TYR cc_start: 0.8135 (m-80) cc_final: 0.7828 (m-10) REVERT: B 107 TYR cc_start: 0.6238 (p90) cc_final: 0.5798 (p90) REVERT: C 38 TYR cc_start: 0.6826 (m-80) cc_final: 0.6482 (m-10) REVERT: C 40 GLN cc_start: 0.8592 (pt0) cc_final: 0.8268 (pm20) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1388 time to fit residues: 4.7642 Evaluate side-chains 22 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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: 9.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** C 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.060205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.051735 restraints weight = 26883.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.053059 restraints weight = 18532.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.054012 restraints weight = 13561.010| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.6993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3004 Z= 0.183 Angle : 0.603 7.707 4112 Z= 0.309 Chirality : 0.044 0.202 472 Planarity : 0.004 0.047 540 Dihedral : 4.292 16.325 454 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.45 % Favored : 92.31 % Rotamer: Outliers : 0.35 % Allowed : 0.00 % 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: -1.11 (0.43), residues: 416 helix: -0.73 (1.05), residues: 25 sheet: 0.44 (0.46), residues: 139 loop : -1.50 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 49 HIS 0.002 0.001 HIS C 33 PHE 0.014 0.001 PHE A 486 TYR 0.012 0.001 TYR B 35 ARG 0.004 0.001 ARG B 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1333.73 seconds wall clock time: 24 minutes 49.99 seconds (1489.99 seconds total)