null Sun 23 Dec 22:22:59 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 2go7-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2go7-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2go7-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.6-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/2go7-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.6-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 ============================================================ Sun 23 Dec 22:23:08 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/2go7-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2go7-3.6-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 810 and 0 Target number of residues in the AU: 810 Target solvent content: 0.6427 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 828 Adjusted target solvent content: 0.63 Input MTZ file: 2go7-3.6-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: 169 Cell parameters: 155.000 155.000 88.440 90.000 90.000 120.000 Input sequence file: 2go7-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 6624 target number of atoms Had to go as low as 1.10 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: 134.234 3.600 Wilson plot Bfac: 73.62 14169 reflections ( 99.78 % complete ) and 0 restraints for refining 7343 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3585 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3452 (Rfree = 0.000) for 7343 atoms. Found 47 (47 requested) and removed 138 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 2.89 Search for helices and strands: 0 residues in 0 chains, 7347 seeds are put forward NCS extension: 0 residues added, 7347 seeds are put forward Round 1: 296 peptides, 61 chains. Longest chain 8 peptides. Score 0.257 Round 2: 395 peptides, 69 chains. Longest chain 10 peptides. Score 0.354 Round 3: 455 peptides, 78 chains. Longest chain 18 peptides. Score 0.383 Round 4: 479 peptides, 82 chains. Longest chain 14 peptides. Score 0.392 Round 5: 494 peptides, 78 chains. Longest chain 15 peptides. Score 0.434 Taking the results from Round 5 Chains 79, Residues 416, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13116 restraints for refining 6004 atoms. 11432 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2767 (Rfree = 0.000) for 6004 atoms. Found 38 (38 requested) and removed 37 (19 requested) atoms. Cycle 2: After refmac, R = 0.2587 (Rfree = 0.000) for 5921 atoms. Found 38 (38 requested) and removed 39 (19 requested) atoms. Cycle 3: After refmac, R = 0.2314 (Rfree = 0.000) for 5894 atoms. Found 9 (37 requested) and removed 30 (18 requested) atoms. Cycle 4: After refmac, R = 0.2369 (Rfree = 0.000) for 5855 atoms. Found 26 (37 requested) and removed 34 (18 requested) atoms. Cycle 5: After refmac, R = 0.2360 (Rfree = 0.000) for 5830 atoms. Found 25 (37 requested) and removed 30 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 2.82 Search for helices and strands: 0 residues in 0 chains, 6115 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 6137 seeds are put forward Round 1: 490 peptides, 83 chains. Longest chain 12 peptides. Score 0.400 Round 2: 508 peptides, 71 chains. Longest chain 21 peptides. Score 0.489 Round 3: 526 peptides, 65 chains. Longest chain 26 peptides. Score 0.541 Round 4: 530 peptides, 65 chains. Longest chain 24 peptides. Score 0.545 Round 5: 509 peptides, 63 chains. Longest chain 22 peptides. Score 0.532 Taking the results from Round 4 Chains 65, Residues 465, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13137 restraints for refining 6003 atoms. 11342 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2398 (Rfree = 0.000) for 6003 atoms. Found 34 (38 requested) and removed 36 (19 requested) atoms. Cycle 7: After refmac, R = 0.2263 (Rfree = 0.000) for 5956 atoms. Found 13 (38 requested) and removed 33 (19 requested) atoms. Cycle 8: After refmac, R = 0.2301 (Rfree = 0.000) for 5914 atoms. Found 19 (38 requested) and removed 30 (19 requested) atoms. Cycle 9: After refmac, R = 0.2263 (Rfree = 0.000) for 5875 atoms. Found 37 (37 requested) and removed 30 (18 requested) atoms. Cycle 10: After refmac, R = 0.2217 (Rfree = 0.000) for 5871 atoms. Found 20 (37 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 2.89 Search for helices and strands: 0 residues in 0 chains, 6194 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 6217 seeds are put forward Round 1: 478 peptides, 77 chains. Longest chain 22 peptides. Score 0.419 Round 2: 513 peptides, 71 chains. Longest chain 18 peptides. Score 0.495 Round 3: 512 peptides, 75 chains. Longest chain 19 peptides. Score 0.473 Round 4: 524 peptides, 66 chains. Longest chain 20 peptides. Score 0.534 Round 5: 527 peptides, 64 chains. Longest chain 28 peptides. Score 0.547 Taking the results from Round 5 Chains 66, Residues 463, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 12883 restraints for refining 6000 atoms. 11054 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2489 (Rfree = 0.000) for 6000 atoms. Found 35 (38 requested) and removed 27 (19 requested) atoms. Cycle 12: After refmac, R = 0.2259 (Rfree = 0.000) for 5942 atoms. Found 24 (38 requested) and removed 24 (19 requested) atoms. Cycle 13: After refmac, R = 0.2198 (Rfree = 0.000) for 5914 atoms. Found 16 (38 requested) and removed 22 (19 requested) atoms. Cycle 14: After refmac, R = 0.2176 (Rfree = 0.000) for 5894 atoms. Found 19 (37 requested) and removed 21 (18 requested) atoms. Cycle 15: After refmac, R = 0.2112 (Rfree = 0.000) for 5877 atoms. Found 15 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 2.89 Search for helices and strands: 0 residues in 0 chains, 6094 seeds are put forward NCS extension: 41 residues added (1 deleted due to clashes), 6135 seeds are put forward Round 1: 445 peptides, 72 chains. Longest chain 15 peptides. Score 0.404 Round 2: 514 peptides, 67 chains. Longest chain 17 peptides. Score 0.517 Round 3: 517 peptides, 61 chains. Longest chain 24 peptides. Score 0.551 Round 4: 509 peptides, 64 chains. Longest chain 26 peptides. Score 0.527 Round 5: 519 peptides, 60 chains. Longest chain 26 peptides. Score 0.559 Taking the results from Round 5 Chains 62, Residues 459, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13140 restraints for refining 6002 atoms. 11334 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2530 (Rfree = 0.000) for 6002 atoms. Found 38 (38 requested) and removed 31 (19 requested) atoms. Cycle 17: After refmac, R = 0.2311 (Rfree = 0.000) for 5978 atoms. Found 34 (38 requested) and removed 37 (19 requested) atoms. Cycle 18: After refmac, R = 0.2181 (Rfree = 0.000) for 5952 atoms. Found 19 (38 requested) and removed 35 (19 requested) atoms. Cycle 19: After refmac, R = 0.2105 (Rfree = 0.000) for 5932 atoms. Found 15 (38 requested) and removed 30 (19 requested) atoms. Cycle 20: After refmac, R = 0.2036 (Rfree = 0.000) for 5911 atoms. Found 15 (37 requested) and removed 27 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.43 2.87 Search for helices and strands: 0 residues in 0 chains, 6148 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 6177 seeds are put forward Round 1: 457 peptides, 69 chains. Longest chain 20 peptides. Score 0.437 Round 2: 487 peptides, 64 chains. Longest chain 23 peptides. Score 0.502 Round 3: 506 peptides, 65 chains. Longest chain 26 peptides. Score 0.519 Round 4: 503 peptides, 61 chains. Longest chain 26 peptides. Score 0.536 Round 5: 494 peptides, 62 chains. Longest chain 25 peptides. Score 0.521 Taking the results from Round 4 Chains 61, Residues 442, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13135 restraints for refining 6001 atoms. 11428 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2419 (Rfree = 0.000) for 6001 atoms. Found 32 (38 requested) and removed 45 (19 requested) atoms. Cycle 22: After refmac, R = 0.2176 (Rfree = 0.000) for 5943 atoms. Found 19 (38 requested) and removed 38 (19 requested) atoms. Cycle 23: After refmac, R = 0.2075 (Rfree = 0.000) for 5893 atoms. Found 15 (38 requested) and removed 27 (19 requested) atoms. Cycle 24: After refmac, R = 0.2047 (Rfree = 0.000) for 5858 atoms. Found 16 (37 requested) and removed 21 (18 requested) atoms. Cycle 25: After refmac, R = 0.1943 (Rfree = 0.000) for 5840 atoms. Found 5 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 2.87 Search for helices and strands: 0 residues in 0 chains, 6058 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 6081 seeds are put forward Round 1: 459 peptides, 79 chains. Longest chain 14 peptides. Score 0.382 Round 2: 478 peptides, 68 chains. Longest chain 22 peptides. Score 0.469 Round 3: 482 peptides, 66 chains. Longest chain 24 peptides. Score 0.485 Round 4: 508 peptides, 67 chains. Longest chain 25 peptides. Score 0.510 Round 5: 499 peptides, 64 chains. Longest chain 24 peptides. Score 0.516 Taking the results from Round 5 Chains 65, Residues 435, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13161 restraints for refining 6003 atoms. 11436 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2482 (Rfree = 0.000) for 6003 atoms. Found 38 (38 requested) and removed 24 (19 requested) atoms. Cycle 27: After refmac, R = 0.2246 (Rfree = 0.000) for 5987 atoms. Found 25 (38 requested) and removed 24 (19 requested) atoms. Cycle 28: After refmac, R = 0.2190 (Rfree = 0.000) for 5973 atoms. Found 20 (38 requested) and removed 20 (19 requested) atoms. Cycle 29: After refmac, R = 0.2129 (Rfree = 0.000) for 5964 atoms. Found 20 (38 requested) and removed 26 (19 requested) atoms. Cycle 30: After refmac, R = 0.1924 (Rfree = 0.000) for 5947 atoms. Found 4 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 2.91 Search for helices and strands: 0 residues in 0 chains, 6226 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6248 seeds are put forward Round 1: 425 peptides, 75 chains. Longest chain 15 peptides. Score 0.359 Round 2: 472 peptides, 65 chains. Longest chain 30 peptides. Score 0.478 Round 3: 483 peptides, 64 chains. Longest chain 31 peptides. Score 0.497 Round 4: 479 peptides, 58 chains. Longest chain 29 peptides. Score 0.524 Round 5: 473 peptides, 61 chains. Longest chain 24 peptides. Score 0.501 Taking the results from Round 4 Chains 58, Residues 421, Estimated correctness of the model 0.0 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13056 restraints for refining 6003 atoms. 11329 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2498 (Rfree = 0.000) for 6003 atoms. Found 38 (38 requested) and removed 26 (19 requested) atoms. Cycle 32: After refmac, R = 0.2450 (Rfree = 0.000) for 5983 atoms. Found 31 (38 requested) and removed 23 (19 requested) atoms. Cycle 33: After refmac, R = 0.2192 (Rfree = 0.000) for 5967 atoms. Found 26 (38 requested) and removed 23 (19 requested) atoms. Cycle 34: After refmac, R = 0.2155 (Rfree = 0.000) for 5951 atoms. Found 24 (38 requested) and removed 19 (19 requested) atoms. Cycle 35: After refmac, R = 0.1939 (Rfree = 0.000) for 5943 atoms. Found 8 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 2.86 Search for helices and strands: 0 residues in 0 chains, 6173 seeds are put forward NCS extension: 46 residues added (1 deleted due to clashes), 6219 seeds are put forward Round 1: 434 peptides, 77 chains. Longest chain 13 peptides. Score 0.360 Round 2: 478 peptides, 69 chains. Longest chain 19 peptides. Score 0.464 Round 3: 458 peptides, 69 chains. Longest chain 16 peptides. Score 0.439 Round 4: 474 peptides, 63 chains. Longest chain 18 peptides. Score 0.492 Round 5: 468 peptides, 67 chains. Longest chain 19 peptides. Score 0.462 Taking the results from Round 4 Chains 63, Residues 411, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13131 restraints for refining 6004 atoms. 11469 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2482 (Rfree = 0.000) for 6004 atoms. Found 36 (38 requested) and removed 21 (19 requested) atoms. Cycle 37: After refmac, R = 0.2233 (Rfree = 0.000) for 5982 atoms. Found 13 (38 requested) and removed 23 (19 requested) atoms. Cycle 38: After refmac, R = 0.2190 (Rfree = 0.000) for 5956 atoms. Found 20 (38 requested) and removed 20 (19 requested) atoms. Cycle 39: After refmac, R = 0.2082 (Rfree = 0.000) for 5939 atoms. Found 19 (38 requested) and removed 21 (19 requested) atoms. Cycle 40: After refmac, R = 0.2035 (Rfree = 0.000) for 5930 atoms. Found 17 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 2.86 Search for helices and strands: 0 residues in 0 chains, 6156 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 6176 seeds are put forward Round 1: 401 peptides, 74 chains. Longest chain 14 peptides. Score 0.332 Round 2: 442 peptides, 71 chains. Longest chain 18 peptides. Score 0.406 Round 3: 445 peptides, 68 chains. Longest chain 17 peptides. Score 0.428 Round 4: 477 peptides, 68 chains. Longest chain 16 peptides. Score 0.468 Round 5: 459 peptides, 63 chains. Longest chain 18 peptides. Score 0.474 Taking the results from Round 5 Chains 63, Residues 396, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13456 restraints for refining 6003 atoms. 11869 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2260 (Rfree = 0.000) for 6003 atoms. Found 38 (38 requested) and removed 25 (19 requested) atoms. Cycle 42: After refmac, R = 0.2043 (Rfree = 0.000) for 5985 atoms. Found 20 (38 requested) and removed 23 (19 requested) atoms. Cycle 43: After refmac, R = 0.1974 (Rfree = 0.000) for 5959 atoms. Found 18 (38 requested) and removed 21 (19 requested) atoms. Cycle 44: After refmac, R = 0.1947 (Rfree = 0.000) for 5948 atoms. Found 20 (38 requested) and removed 23 (19 requested) atoms. Cycle 45: After refmac, R = 0.1896 (Rfree = 0.000) for 5936 atoms. Found 17 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.42 2.86 Search for helices and strands: 0 residues in 0 chains, 6198 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 6213 seeds are put forward Round 1: 357 peptides, 66 chains. Longest chain 12 peptides. Score 0.318 Round 2: 423 peptides, 63 chains. Longest chain 14 peptides. Score 0.428 Round 3: 433 peptides, 68 chains. Longest chain 17 peptides. Score 0.412 Round 4: 437 peptides, 68 chains. Longest chain 18 peptides. Score 0.417 Round 5: 442 peptides, 66 chains. Longest chain 19 peptides. Score 0.435 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 376, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 2go7-3_warpNtrace.pdb as input Building loops using Loopy2018 66 chains (376 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14169 reflections ( 99.78 % complete ) and 13695 restraints for refining 6003 atoms. 12230 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2166 (Rfree = 0.000) for 6003 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2142 (Rfree = 0.000) for 5966 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2116 (Rfree = 0.000) for 5937 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.2056 (Rfree = 0.000) for 5904 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:47:51 GMT 2018 Job finished. TimeTaking 84.88 Used memory is bytes: 1292400