Tue 25 Dec 19:27:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vqr-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vqr-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vqr-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:05 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vqr-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 885 and 0 Target number of residues in the AU: 885 Target solvent content: 0.6181 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.49 Input MTZ file: 1vqr-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 5 Cell parameters: 123.141 122.090 96.897 90.000 120.583 90.000 Input sequence file: 1vqr-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 9504 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 83.418 3.600 Wilson plot Bfac: 60.50 12846 reflections ( 89.37 % complete ) and 0 restraints for refining 10523 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3641 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3184 (Rfree = 0.000) for 10523 atoms. Found 67 (67 requested) and removed 166 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.25 3.29 Search for helices and strands: 0 residues in 0 chains, 10518 seeds are put forward NCS extension: 0 residues added, 10518 seeds are put forward Round 1: 249 peptides, 59 chains. Longest chain 7 peptides. Score 0.190 Round 2: 336 peptides, 72 chains. Longest chain 10 peptides. Score 0.245 Round 3: 387 peptides, 79 chains. Longest chain 8 peptides. Score 0.278 Round 4: 393 peptides, 79 chains. Longest chain 9 peptides. Score 0.287 Round 5: 402 peptides, 78 chains. Longest chain 10 peptides. Score 0.306 Taking the results from Round 5 Chains 78, Residues 324, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 21537 restraints for refining 8614 atoms. 20269 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2565 (Rfree = 0.000) for 8614 atoms. Found 28 (55 requested) and removed 64 (27 requested) atoms. Cycle 2: After refmac, R = 0.2446 (Rfree = 0.000) for 8498 atoms. Found 43 (55 requested) and removed 46 (27 requested) atoms. Cycle 3: After refmac, R = 0.2330 (Rfree = 0.000) for 8457 atoms. Found 47 (54 requested) and removed 46 (27 requested) atoms. Cycle 4: After refmac, R = 0.2231 (Rfree = 0.000) for 8419 atoms. Found 49 (54 requested) and removed 41 (27 requested) atoms. Cycle 5: After refmac, R = 0.1883 (Rfree = 0.000) for 8410 atoms. Found 7 (54 requested) and removed 34 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.29 Search for helices and strands: 0 residues in 0 chains, 8541 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 8553 seeds are put forward Round 1: 402 peptides, 87 chains. Longest chain 9 peptides. Score 0.251 Round 2: 466 peptides, 93 chains. Longest chain 13 peptides. Score 0.307 Round 3: 473 peptides, 90 chains. Longest chain 11 peptides. Score 0.334 Round 4: 447 peptides, 80 chains. Longest chain 12 peptides. Score 0.357 Round 5: 447 peptides, 83 chains. Longest chain 14 peptides. Score 0.339 Taking the results from Round 4 Chains 80, Residues 367, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12846 reflections ( 89.37 % complete ) and 20755 restraints for refining 8516 atoms. 19344 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2268 (Rfree = 0.000) for 8516 atoms. Found 40 (54 requested) and removed 69 (27 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2093 (Rfree = 0.000) for 8439 atoms. Found 32 (54 requested) and removed 48 (27 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1774 (Rfree = 0.000) for 8398 atoms. Found 11 (54 requested) and removed 36 (27 requested) atoms. Cycle 9: After refmac, R = 0.1802 (Rfree = 0.000) for 8359 atoms. Found 14 (53 requested) and removed 31 (26 requested) atoms. Cycle 10: After refmac, R = 0.1671 (Rfree = 0.000) for 8335 atoms. Found 9 (53 requested) and removed 31 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.26 Search for helices and strands: 0 residues in 0 chains, 8529 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 8543 seeds are put forward Round 1: 420 peptides, 88 chains. Longest chain 8 peptides. Score 0.271 Round 2: 478 peptides, 88 chains. Longest chain 12 peptides. Score 0.352 Round 3: 459 peptides, 82 chains. Longest chain 11 peptides. Score 0.362 Round 4: 465 peptides, 79 chains. Longest chain 10 peptides. Score 0.387 Round 5: 466 peptides, 79 chains. Longest chain 14 peptides. Score 0.388 Taking the results from Round 5 Chains 79, Residues 387, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 20848 restraints for refining 8615 atoms. 19360 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2116 (Rfree = 0.000) for 8615 atoms. Found 48 (55 requested) and removed 56 (27 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2033 (Rfree = 0.000) for 8564 atoms. Found 41 (55 requested) and removed 49 (27 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1969 (Rfree = 0.000) for 8530 atoms. Found 37 (54 requested) and removed 36 (27 requested) atoms. Cycle 14: After refmac, R = 0.1902 (Rfree = 0.000) for 8511 atoms. Found 43 (54 requested) and removed 49 (27 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1811 (Rfree = 0.000) for 8487 atoms. Found 29 (54 requested) and removed 36 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.27 3.31 Search for helices and strands: 0 residues in 0 chains, 8679 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 8698 seeds are put forward Round 1: 400 peptides, 82 chains. Longest chain 9 peptides. Score 0.279 Round 2: 447 peptides, 81 chains. Longest chain 14 peptides. Score 0.351 Round 3: 464 peptides, 81 chains. Longest chain 12 peptides. Score 0.374 Round 4: 471 peptides, 81 chains. Longest chain 13 peptides. Score 0.383 Round 5: 450 peptides, 76 chains. Longest chain 12 peptides. Score 0.384 Taking the results from Round 5 Chains 76, Residues 374, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 20784 restraints for refining 8610 atoms. 19347 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1984 (Rfree = 0.000) for 8610 atoms. Found 37 (55 requested) and removed 43 (27 requested) atoms. Cycle 17: After refmac, R = 0.1825 (Rfree = 0.000) for 8567 atoms. Found 13 (55 requested) and removed 33 (27 requested) atoms. Cycle 18: After refmac, R = 0.1750 (Rfree = 0.000) for 8536 atoms. Found 10 (54 requested) and removed 34 (27 requested) atoms. Cycle 19: After refmac, R = 0.1689 (Rfree = 0.000) for 8509 atoms. Found 3 (54 requested) and removed 31 (27 requested) atoms. Cycle 20: After refmac, R = 0.1664 (Rfree = 0.000) for 8473 atoms. Found 4 (54 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.33 Search for helices and strands: 0 residues in 0 chains, 8575 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8590 seeds are put forward Round 1: 398 peptides, 79 chains. Longest chain 15 peptides. Score 0.294 Round 2: 456 peptides, 83 chains. Longest chain 14 peptides. Score 0.352 Round 3: 438 peptides, 77 chains. Longest chain 15 peptides. Score 0.362 Round 4: 425 peptides, 69 chains. Longest chain 16 peptides. Score 0.392 Round 5: 440 peptides, 70 chains. Longest chain 17 peptides. Score 0.406 Taking the results from Round 5 Chains 70, Residues 370, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 20805 restraints for refining 8613 atoms. 19380 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2020 (Rfree = 0.000) for 8613 atoms. Found 27 (55 requested) and removed 43 (27 requested) atoms. Cycle 22: After refmac, R = 0.1883 (Rfree = 0.000) for 8566 atoms. Found 33 (55 requested) and removed 30 (27 requested) atoms. Cycle 23: After refmac, R = 0.1958 (Rfree = 0.000) for 8545 atoms. Found 30 (54 requested) and removed 35 (27 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1840 (Rfree = 0.000) for 8521 atoms. Found 29 (54 requested) and removed 33 (27 requested) atoms. Cycle 25: After refmac, R = 0.1592 (Rfree = 0.000) for 8503 atoms. Found 9 (54 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.33 Search for helices and strands: 0 residues in 0 chains, 8665 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 8687 seeds are put forward Round 1: 380 peptides, 81 chains. Longest chain 9 peptides. Score 0.255 Round 2: 431 peptides, 80 chains. Longest chain 13 peptides. Score 0.335 Round 3: 462 peptides, 82 chains. Longest chain 14 peptides. Score 0.366 Round 4: 441 peptides, 72 chains. Longest chain 15 peptides. Score 0.396 Round 5: 439 peptides, 73 chains. Longest chain 14 peptides. Score 0.387 Taking the results from Round 4 Chains 72, Residues 369, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 20662 restraints for refining 8615 atoms. 19234 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1942 (Rfree = 0.000) for 8615 atoms. Found 41 (55 requested) and removed 33 (27 requested) atoms. Cycle 27: After refmac, R = 0.1881 (Rfree = 0.000) for 8594 atoms. Found 26 (55 requested) and removed 35 (27 requested) atoms. Cycle 28: After refmac, R = 0.1844 (Rfree = 0.000) for 8577 atoms. Found 22 (55 requested) and removed 28 (27 requested) atoms. Cycle 29: After refmac, R = 0.1761 (Rfree = 0.000) for 8564 atoms. Found 23 (54 requested) and removed 30 (27 requested) atoms. Cycle 30: After refmac, R = 0.1726 (Rfree = 0.000) for 8547 atoms. Found 16 (54 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.29 3.33 Search for helices and strands: 0 residues in 0 chains, 8697 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 8713 seeds are put forward Round 1: 374 peptides, 83 chains. Longest chain 10 peptides. Score 0.233 Round 2: 407 peptides, 78 chains. Longest chain 12 peptides. Score 0.313 Round 3: 401 peptides, 73 chains. Longest chain 14 peptides. Score 0.335 Round 4: 429 peptides, 75 chains. Longest chain 16 peptides. Score 0.362 Round 5: 401 peptides, 70 chains. Longest chain 15 peptides. Score 0.353 Taking the results from Round 4 Chains 75, Residues 354, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 20764 restraints for refining 8615 atoms. 19381 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2004 (Rfree = 0.000) for 8615 atoms. Found 54 (55 requested) and removed 34 (27 requested) atoms. Cycle 32: After refmac, R = 0.1850 (Rfree = 0.000) for 8612 atoms. Found 23 (55 requested) and removed 31 (27 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1861 (Rfree = 0.000) for 8590 atoms. Found 31 (55 requested) and removed 36 (27 requested) atoms. Cycle 34: After refmac, R = 0.1827 (Rfree = 0.000) for 8574 atoms. Found 30 (55 requested) and removed 34 (27 requested) atoms. Cycle 35: After refmac, R = 0.1810 (Rfree = 0.000) for 8562 atoms. Found 37 (54 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.34 Search for helices and strands: 0 residues in 0 chains, 8729 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 8752 seeds are put forward Round 1: 385 peptides, 85 chains. Longest chain 11 peptides. Score 0.237 Round 2: 377 peptides, 72 chains. Longest chain 10 peptides. Score 0.307 Round 3: 388 peptides, 73 chains. Longest chain 11 peptides. Score 0.317 Round 4: 387 peptides, 73 chains. Longest chain 13 peptides. Score 0.315 Round 5: 403 peptides, 75 chains. Longest chain 12 peptides. Score 0.326 Taking the results from Round 5 Chains 75, Residues 328, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 20973 restraints for refining 8614 atoms. 19718 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1924 (Rfree = 0.000) for 8614 atoms. Found 38 (55 requested) and removed 33 (27 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1853 (Rfree = 0.000) for 8598 atoms. Found 33 (55 requested) and removed 29 (27 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1885 (Rfree = 0.000) for 8588 atoms. Found 36 (55 requested) and removed 30 (27 requested) atoms. Cycle 39: After refmac, R = 0.1818 (Rfree = 0.000) for 8585 atoms. Found 34 (55 requested) and removed 30 (27 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1850 (Rfree = 0.000) for 8578 atoms. Found 33 (55 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 3.36 Search for helices and strands: 0 residues in 0 chains, 8762 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 8775 seeds are put forward Round 1: 316 peptides, 71 chains. Longest chain 7 peptides. Score 0.220 Round 2: 343 peptides, 69 chains. Longest chain 11 peptides. Score 0.276 Round 3: 351 peptides, 72 chains. Longest chain 11 peptides. Score 0.268 Round 4: 347 peptides, 65 chains. Longest chain 12 peptides. Score 0.307 Round 5: 369 peptides, 66 chains. Longest chain 12 peptides. Score 0.333 Taking the results from Round 5 Chains 66, Residues 303, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12846 reflections ( 89.37 % complete ) and 21045 restraints for refining 8615 atoms. 19899 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1916 (Rfree = 0.000) for 8615 atoms. Found 34 (55 requested) and removed 34 (27 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1864 (Rfree = 0.000) for 8597 atoms. Found 34 (55 requested) and removed 39 (27 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1785 (Rfree = 0.000) for 8584 atoms. Found 22 (55 requested) and removed 31 (27 requested) atoms. Cycle 44: After refmac, R = 0.1745 (Rfree = 0.000) for 8564 atoms. Found 24 (55 requested) and removed 28 (27 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1736 (Rfree = 0.000) for 8557 atoms. Found 27 (54 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.33 Search for helices and strands: 0 residues in 0 chains, 8731 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 8744 seeds are put forward Round 1: 333 peptides, 72 chains. Longest chain 9 peptides. Score 0.241 Round 2: 371 peptides, 74 chains. Longest chain 10 peptides. Score 0.286 Round 3: 353 peptides, 69 chains. Longest chain 11 peptides. Score 0.291 Round 4: 372 peptides, 68 chains. Longest chain 12 peptides. Score 0.325 Round 5: 346 peptides, 60 chains. Longest chain 14 peptides. Score 0.338 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 286, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vqr-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12846 reflections ( 89.37 % complete ) and 21128 restraints for refining 8615 atoms. 20044 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1892 (Rfree = 0.000) for 8615 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.1780 (Rfree = 0.000) for 8573 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.1775 (Rfree = 0.000) for 8534 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.1733 (Rfree = 0.000) for 8497 atoms. Found 0 (54 requested) and removed 27 (27 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 21:31:58 GMT 2018 Job finished. TimeTaking 124.04