Starting phenix.real_space_refine on Mon Feb 10 20:25:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b6e_12053/02_2025/7b6e_12053.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b6e_12053/02_2025/7b6e_12053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b6e_12053/02_2025/7b6e_12053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b6e_12053/02_2025/7b6e_12053.map" model { file = "/net/cci-nas-00/data/ceres_data/7b6e_12053/02_2025/7b6e_12053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b6e_12053/02_2025/7b6e_12053.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 13 5.16 5 C 1406 2.51 5 N 389 2.21 5 O 397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2205 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2205 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 4, 'TRANS': 264} Chain breaks: 1 Time building chain proxies: 2.89, per 1000 atoms: 1.31 Number of scatterers: 2205 At special positions: 0 Unit cell: (63.648, 73.632, 92.352, 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 13 16.00 O 397 8.00 N 389 7.00 C 1406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.62 Conformation dependent library (CDL) restraints added in 263.6 milliseconds 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 522 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 86.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 355 through 384 removed outlier: 4.194A pdb=" N HIS A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 425 through 438 removed outlier: 4.158A pdb=" N PHE A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 456 Processing helix chain 'A' and resid 461 through 477 Processing helix chain 'A' and resid 483 through 500 removed outlier: 3.762A pdb=" N THR A 498 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 removed outlier: 4.176A pdb=" N ALA A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.905A pdb=" N ASN A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 557 removed outlier: 3.726A pdb=" N THR A 556 " --> pdb=" O CYS A 552 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 579 removed outlier: 4.874A pdb=" N ARG A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 598 removed outlier: 3.665A pdb=" N ARG A 598 " --> pdb=" O VAL A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 614 removed outlier: 4.015A pdb=" N GLU A 604 " --> pdb=" O TRP A 600 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 632 removed outlier: 4.487A pdb=" N ALA A 624 " --> pdb=" O GLN A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 661 165 hydrogen bonds defined for protein. 495 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: 0.59 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 691 1.34 - 1.46: 378 1.46 - 1.57: 1162 1.57 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 2252 Sorted by residual: bond pdb=" CB PRO A 559 " pdb=" CG PRO A 559 " ideal model delta sigma weight residual 1.492 1.555 -0.063 5.00e-02 4.00e+02 1.59e+00 bond pdb=" CG PRO A 559 " pdb=" CD PRO A 559 " ideal model delta sigma weight residual 1.503 1.542 -0.039 3.40e-02 8.65e+02 1.32e+00 bond pdb=" CB PHE A 436 " pdb=" CG PHE A 436 " ideal model delta sigma weight residual 1.502 1.476 0.026 2.30e-02 1.89e+03 1.30e+00 bond pdb=" N TRP A 600 " pdb=" CA TRP A 600 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.20e+00 bond pdb=" CG LEU A 468 " pdb=" CD2 LEU A 468 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 ... (remaining 2247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 2967 2.79 - 5.59: 63 5.59 - 8.38: 3 8.38 - 11.17: 3 11.17 - 13.96: 1 Bond angle restraints: 3037 Sorted by residual: angle pdb=" CA PRO A 559 " pdb=" N PRO A 559 " pdb=" CD PRO A 559 " ideal model delta sigma weight residual 112.00 102.11 9.89 1.40e+00 5.10e-01 4.99e+01 angle pdb=" C LEU A 434 " pdb=" N TYR A 435 " pdb=" CA TYR A 435 " ideal model delta sigma weight residual 121.58 113.58 8.00 1.95e+00 2.63e-01 1.68e+01 angle pdb=" CA LEU A 468 " pdb=" CB LEU A 468 " pdb=" CG LEU A 468 " ideal model delta sigma weight residual 116.30 130.26 -13.96 3.50e+00 8.16e-02 1.59e+01 angle pdb=" CA ARG A 508 " pdb=" CB ARG A 508 " pdb=" CG ARG A 508 " ideal model delta sigma weight residual 114.10 122.05 -7.95 2.00e+00 2.50e-01 1.58e+01 angle pdb=" C ALA A 467 " pdb=" N LEU A 468 " pdb=" CA LEU A 468 " ideal model delta sigma weight residual 120.31 115.02 5.29 1.52e+00 4.33e-01 1.21e+01 ... (remaining 3032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 1143 15.16 - 30.32: 169 30.32 - 45.48: 35 45.48 - 60.64: 2 60.64 - 75.79: 4 Dihedral angle restraints: 1353 sinusoidal: 544 harmonic: 809 Sorted by residual: dihedral pdb=" CA ARG A 598 " pdb=" C ARG A 598 " pdb=" N GLU A 599 " pdb=" CA GLU A 599 " ideal model delta harmonic sigma weight residual -180.00 -145.66 -34.34 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA SER A 538 " pdb=" C SER A 538 " pdb=" N ASP A 539 " pdb=" CA ASP A 539 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLN A 482 " pdb=" C GLN A 482 " pdb=" N ARG A 483 " pdb=" CA ARG A 483 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 1350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 199 0.041 - 0.082: 93 0.082 - 0.123: 23 0.123 - 0.165: 6 0.165 - 0.206: 5 Chirality restraints: 326 Sorted by residual: chirality pdb=" CA GLN A 529 " pdb=" N GLN A 529 " pdb=" C GLN A 529 " pdb=" CB GLN A 529 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ARG A 508 " pdb=" N ARG A 508 " pdb=" C ARG A 508 " pdb=" CB ARG A 508 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA GLU A 469 " pdb=" N GLU A 469 " pdb=" C GLU A 469 " pdb=" CB GLU A 469 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 323 not shown) Planarity restraints: 388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 558 " 0.075 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO A 559 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 559 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 559 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 547 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" CD GLU A 547 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A 547 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 547 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 508 " -0.039 9.50e-02 1.11e+02 2.36e-02 3.33e+00 pdb=" NE ARG A 508 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 508 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 508 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 508 " 0.009 2.00e-02 2.50e+03 ... (remaining 385 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 90 2.68 - 3.24: 2676 3.24 - 3.79: 3824 3.79 - 4.35: 5131 4.35 - 4.90: 7212 Nonbonded interactions: 18933 Sorted by model distance: nonbonded pdb=" O ALA A 471 " pdb=" OG SER A 474 " model vdw 2.129 3.040 nonbonded pdb=" OE1 GLN A 482 " pdb=" NZ LYS A 484 " model vdw 2.161 3.120 nonbonded pdb=" O CYS A 516 " pdb=" OG1 THR A 519 " model vdw 2.178 3.040 nonbonded pdb=" O GLU A 382 " pdb=" OG1 THR A 385 " model vdw 2.191 3.040 nonbonded pdb=" O ALA A 612 " pdb=" N TYR A 616 " model vdw 2.203 3.120 ... (remaining 18928 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: 2.590 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.580 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 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 : 0.005 0.063 2252 Z= 0.309 Angle : 1.026 13.963 3037 Z= 0.575 Chirality : 0.053 0.206 326 Planarity : 0.007 0.108 388 Dihedral : 15.044 75.794 831 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 36.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -3.88 (0.43), residues: 265 helix: -2.02 (0.29), residues: 225 sheet: None (None), residues: 0 loop : -4.52 (0.69), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 600 HIS 0.007 0.002 HIS A 561 PHE 0.015 0.003 PHE A 628 TYR 0.026 0.002 TYR A 435 ARG 0.031 0.002 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.255 Fit side-chains REVERT: A 477 MET cc_start: 0.8355 (ptp) cc_final: 0.7803 (pmm) REVERT: A 484 LYS cc_start: 0.9700 (ptpp) cc_final: 0.9389 (pttp) REVERT: A 606 HIS cc_start: 0.8591 (m-70) cc_final: 0.8297 (m-70) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1935 time to fit residues: 6.7174 Evaluate side-chains 24 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.063722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.054250 restraints weight = 19138.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.055691 restraints weight = 13230.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.056725 restraints weight = 9718.919| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2252 Z= 0.241 Angle : 0.899 13.323 3037 Z= 0.462 Chirality : 0.048 0.179 326 Planarity : 0.005 0.040 388 Dihedral : 6.881 25.390 306 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % 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: -2.65 (0.46), residues: 265 helix: -1.11 (0.32), residues: 221 sheet: None (None), residues: 0 loop : -4.34 (0.70), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 600 HIS 0.004 0.001 HIS A 561 PHE 0.030 0.003 PHE A 628 TYR 0.024 0.002 TYR A 435 ARG 0.008 0.001 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 530 LEU cc_start: 0.9277 (mm) cc_final: 0.8905 (tp) REVERT: A 552 CYS cc_start: 0.9201 (m) cc_final: 0.8825 (m) REVERT: A 606 HIS cc_start: 0.8470 (m-70) cc_final: 0.8202 (m-70) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2026 time to fit residues: 7.6733 Evaluate side-chains 26 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.063992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.054402 restraints weight = 19171.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.055772 restraints weight = 13207.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.056787 restraints weight = 9757.082| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2252 Z= 0.221 Angle : 0.894 13.338 3037 Z= 0.455 Chirality : 0.047 0.178 326 Planarity : 0.005 0.038 388 Dihedral : 6.668 26.089 306 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % 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: -2.23 (0.47), residues: 265 helix: -0.84 (0.32), residues: 221 sheet: None (None), residues: 0 loop : -4.13 (0.72), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 600 HIS 0.003 0.001 HIS A 567 PHE 0.012 0.002 PHE A 553 TYR 0.025 0.002 TYR A 488 ARG 0.004 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 484 LYS cc_start: 0.9396 (pttm) cc_final: 0.8940 (pttp) REVERT: A 508 ARG cc_start: 0.8760 (ptt-90) cc_final: 0.8401 (ptp-170) REVERT: A 514 MET cc_start: 0.8367 (tmm) cc_final: 0.8078 (tmm) REVERT: A 533 MET cc_start: 0.7311 (ttt) cc_final: 0.6993 (ttt) REVERT: A 552 CYS cc_start: 0.9095 (m) cc_final: 0.8752 (m) REVERT: A 606 HIS cc_start: 0.8430 (m-70) cc_final: 0.8113 (m90) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2271 time to fit residues: 8.7678 Evaluate side-chains 28 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 0.0470 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.070501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.061760 restraints weight = 19614.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.063237 restraints weight = 12525.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.064287 restraints weight = 8754.617| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2252 Z= 0.219 Angle : 0.891 13.638 3037 Z= 0.450 Chirality : 0.045 0.178 326 Planarity : 0.004 0.035 388 Dihedral : 6.504 24.417 306 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % 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: -1.84 (0.48), residues: 265 helix: -0.52 (0.33), residues: 221 sheet: None (None), residues: 0 loop : -4.35 (0.66), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 600 HIS 0.003 0.001 HIS A 567 PHE 0.012 0.002 PHE A 553 TYR 0.037 0.002 TYR A 488 ARG 0.003 0.000 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 508 ARG cc_start: 0.8686 (ptt-90) cc_final: 0.8335 (ptp-170) REVERT: A 606 HIS cc_start: 0.8375 (m-70) cc_final: 0.8074 (m90) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2260 time to fit residues: 8.7330 Evaluate side-chains 24 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.5255 > 50: distance: 5 - 20: 28.067 distance: 16 - 20: 29.124 distance: 20 - 21: 18.389 distance: 21 - 22: 53.541 distance: 21 - 24: 15.488 distance: 22 - 23: 64.154 distance: 22 - 28: 13.391 distance: 24 - 25: 19.381 distance: 25 - 26: 31.769 distance: 25 - 27: 22.594 distance: 28 - 29: 12.209 distance: 29 - 30: 55.201 distance: 29 - 32: 65.525 distance: 30 - 31: 38.836 distance: 30 - 39: 22.350 distance: 32 - 33: 37.038 distance: 33 - 34: 21.263 distance: 34 - 35: 6.976 distance: 35 - 36: 6.059 distance: 36 - 38: 3.128 distance: 39 - 40: 34.009 distance: 39 - 45: 33.134 distance: 40 - 41: 14.833 distance: 40 - 43: 28.781 distance: 41 - 42: 38.300 distance: 41 - 46: 17.768 distance: 43 - 44: 25.940 distance: 44 - 45: 35.909 distance: 46 - 47: 25.257 distance: 47 - 48: 21.458 distance: 48 - 49: 20.226 distance: 48 - 50: 38.008 distance: 50 - 51: 30.423 distance: 51 - 52: 38.875 distance: 51 - 54: 16.834 distance: 52 - 53: 28.223 distance: 52 - 56: 45.366 distance: 54 - 55: 43.811 distance: 56 - 57: 23.605 distance: 57 - 58: 5.673 distance: 57 - 60: 60.972 distance: 58 - 59: 19.193 distance: 58 - 64: 43.531 distance: 60 - 61: 23.519 distance: 61 - 62: 31.612 distance: 61 - 63: 34.458 distance: 64 - 65: 32.996 distance: 65 - 66: 39.591 distance: 65 - 68: 32.566 distance: 66 - 67: 18.957 distance: 66 - 73: 24.582 distance: 68 - 69: 39.204 distance: 69 - 70: 27.326 distance: 70 - 71: 19.725 distance: 70 - 72: 10.232 distance: 73 - 74: 28.926 distance: 74 - 75: 62.637 distance: 74 - 77: 3.910 distance: 75 - 76: 10.798 distance: 75 - 79: 24.145 distance: 76 - 102: 24.806 distance: 77 - 78: 47.875 distance: 79 - 80: 19.386 distance: 80 - 81: 19.562 distance: 80 - 83: 21.269 distance: 81 - 82: 22.314 distance: 81 - 84: 28.915 distance: 82 - 111: 22.971 distance: 84 - 85: 22.528 distance: 85 - 86: 23.015 distance: 85 - 88: 29.693 distance: 86 - 87: 40.013 distance: 86 - 93: 26.332 distance: 87 - 118: 29.985 distance: 88 - 89: 28.624 distance: 89 - 90: 29.221 distance: 90 - 91: 18.137 distance: 90 - 92: 9.221