null Sun 23 Dec 22:22:41 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 2g0t-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2g0t-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2g0t-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2g0t-3.4-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/2g0t-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2g0t-3.4-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 22:22:50 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/2g0t-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2g0t-3.4-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 924 and 0 Target number of residues in the AU: 924 Target solvent content: 0.5732 Checking the provided sequence file Detected sequence length: 350 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 700 Adjusted target solvent content: 0.68 Input MTZ file: 2g0t-3.4-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: 213 Cell parameters: 191.568 191.568 191.568 90.000 90.000 90.000 Input sequence file: 2g0t-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 5600 target number of atoms Had to go as low as 0.95 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: 29.560 3.400 Wilson plot Bfac: 42.73 17072 reflections ( 99.75 % complete ) and 0 restraints for refining 6184 atoms. Observations/parameters ratio is 0.69 ------------------------------------------------------ Starting model: R = 0.3185 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2494 (Rfree = 0.000) for 6184 atoms. Found 46 (46 requested) and removed 44 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.90 2.26 Search for helices and strands: 0 residues in 0 chains, 6322 seeds are put forward NCS extension: 0 residues added, 6322 seeds are put forward Round 1: 464 peptides, 63 chains. Longest chain 28 peptides. Score 0.490 Round 2: 509 peptides, 57 chains. Longest chain 37 peptides. Score 0.575 Round 3: 537 peptides, 55 chains. Longest chain 45 peptides. Score 0.614 Round 4: 517 peptides, 53 chains. Longest chain 25 peptides. Score 0.603 Round 5: 518 peptides, 51 chains. Longest chain 36 peptides. Score 0.614 Taking the results from Round 5 Chains 53, Residues 467, Estimated correctness of the model 33.2 % 10 chains (141 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 9278 restraints for refining 5161 atoms. 6927 conditional restraints added. Observations/parameters ratio is 0.83 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2697 (Rfree = 0.000) for 5161 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 2: After refmac, R = 0.2543 (Rfree = 0.000) for 5070 atoms. Found 38 (38 requested) and removed 32 (19 requested) atoms. Cycle 3: After refmac, R = 0.2446 (Rfree = 0.000) for 5041 atoms. Found 38 (38 requested) and removed 29 (19 requested) atoms. Cycle 4: After refmac, R = 0.2363 (Rfree = 0.000) for 5029 atoms. Found 30 (38 requested) and removed 26 (19 requested) atoms. Cycle 5: After refmac, R = 0.2307 (Rfree = 0.000) for 5023 atoms. Found 23 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.91 2.26 Search for helices and strands: 0 residues in 0 chains, 5191 seeds are put forward NCS extension: 22 residues added (6 deleted due to clashes), 5213 seeds are put forward Round 1: 505 peptides, 50 chains. Longest chain 39 peptides. Score 0.606 Round 2: 534 peptides, 49 chains. Longest chain 39 peptides. Score 0.640 Round 3: 551 peptides, 51 chains. Longest chain 51 peptides. Score 0.647 Round 4: 543 peptides, 54 chains. Longest chain 37 peptides. Score 0.625 Round 5: 560 peptides, 55 chains. Longest chain 38 peptides. Score 0.637 Taking the results from Round 3 Chains 56, Residues 500, Estimated correctness of the model 43.3 % 9 chains (140 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 9092 restraints for refining 5092 atoms. 6650 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2714 (Rfree = 0.000) for 5092 atoms. Found 38 (38 requested) and removed 32 (19 requested) atoms. Cycle 7: After refmac, R = 0.2498 (Rfree = 0.000) for 5065 atoms. Found 38 (38 requested) and removed 29 (19 requested) atoms. Cycle 8: After refmac, R = 0.2371 (Rfree = 0.000) for 5062 atoms. Found 30 (38 requested) and removed 22 (19 requested) atoms. Cycle 9: After refmac, R = 0.2287 (Rfree = 0.000) for 5055 atoms. Found 19 (38 requested) and removed 21 (19 requested) atoms. Cycle 10: After refmac, R = 0.2237 (Rfree = 0.000) for 5041 atoms. Found 22 (38 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.91 2.26 Search for helices and strands: 0 residues in 0 chains, 5212 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 5245 seeds are put forward Round 1: 519 peptides, 51 chains. Longest chain 37 peptides. Score 0.615 Round 2: 547 peptides, 45 chains. Longest chain 35 peptides. Score 0.670 Round 3: 552 peptides, 46 chains. Longest chain 40 peptides. Score 0.670 Round 4: 569 peptides, 46 chains. Longest chain 34 peptides. Score 0.685 Round 5: 562 peptides, 46 chains. Longest chain 49 peptides. Score 0.679 Taking the results from Round 4 Chains 52, Residues 523, Estimated correctness of the model 53.9 % 9 chains (138 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8893 restraints for refining 5091 atoms. 6307 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2687 (Rfree = 0.000) for 5091 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 12: After refmac, R = 0.2500 (Rfree = 0.000) for 5050 atoms. Found 38 (38 requested) and removed 27 (19 requested) atoms. Cycle 13: After refmac, R = 0.2387 (Rfree = 0.000) for 5040 atoms. Found 31 (38 requested) and removed 26 (19 requested) atoms. Cycle 14: After refmac, R = 0.2333 (Rfree = 0.000) for 5030 atoms. Found 19 (38 requested) and removed 29 (19 requested) atoms. Cycle 15: After refmac, R = 0.2290 (Rfree = 0.000) for 5012 atoms. Found 25 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.88 2.24 Search for helices and strands: 0 residues in 0 chains, 5167 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 5179 seeds are put forward Round 1: 539 peptides, 61 chains. Longest chain 25 peptides. Score 0.587 Round 2: 560 peptides, 51 chains. Longest chain 29 peptides. Score 0.655 Round 3: 549 peptides, 49 chains. Longest chain 29 peptides. Score 0.654 Round 4: 563 peptides, 52 chains. Longest chain 29 peptides. Score 0.654 Round 5: 551 peptides, 51 chains. Longest chain 29 peptides. Score 0.647 Taking the results from Round 2 Chains 58, Residues 509, Estimated correctness of the model 45.6 % 15 chains (191 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8765 restraints for refining 5092 atoms. 6061 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2647 (Rfree = 0.000) for 5092 atoms. Found 38 (38 requested) and removed 48 (19 requested) atoms. Cycle 17: After refmac, R = 0.2432 (Rfree = 0.000) for 5062 atoms. Found 38 (38 requested) and removed 26 (19 requested) atoms. Cycle 18: After refmac, R = 0.2305 (Rfree = 0.000) for 5057 atoms. Found 38 (38 requested) and removed 28 (19 requested) atoms. Cycle 19: After refmac, R = 0.2221 (Rfree = 0.000) for 5058 atoms. Found 24 (38 requested) and removed 27 (19 requested) atoms. Cycle 20: After refmac, R = 0.2149 (Rfree = 0.000) for 5042 atoms. Found 26 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.88 2.24 Search for helices and strands: 0 residues in 0 chains, 5206 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 5228 seeds are put forward Round 1: 541 peptides, 51 chains. Longest chain 34 peptides. Score 0.637 Round 2: 565 peptides, 41 chains. Longest chain 49 peptides. Score 0.703 Round 3: 557 peptides, 46 chains. Longest chain 43 peptides. Score 0.675 Round 4: 558 peptides, 43 chains. Longest chain 33 peptides. Score 0.688 Round 5: 563 peptides, 48 chains. Longest chain 41 peptides. Score 0.671 Taking the results from Round 2 Chains 49, Residues 524, Estimated correctness of the model 58.6 % 14 chains (254 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 263 A and 269 A Built loop between residues 102 B and 113 B Built loop between residues 271 B and 274 B 43 chains (535 residues) following loop building 11 chains (271 residues) in sequence following loop building ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 7700 restraints for refining 5091 atoms. 4647 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2676 (Rfree = 0.000) for 5091 atoms. Found 38 (38 requested) and removed 50 (19 requested) atoms. Cycle 22: After refmac, R = 0.2418 (Rfree = 0.000) for 5049 atoms. Found 37 (37 requested) and removed 31 (19 requested) atoms. Cycle 23: After refmac, R = 0.2296 (Rfree = 0.000) for 5046 atoms. Found 26 (36 requested) and removed 27 (19 requested) atoms. Cycle 24: After refmac, R = 0.2236 (Rfree = 0.000) for 5036 atoms. Found 14 (36 requested) and removed 24 (19 requested) atoms. Cycle 25: After refmac, R = 0.2217 (Rfree = 0.000) for 5019 atoms. Found 20 (34 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.89 2.25 Search for helices and strands: 0 residues in 0 chains, 5173 seeds are put forward NCS extension: 32 residues added (8 deleted due to clashes), 5205 seeds are put forward Round 1: 531 peptides, 55 chains. Longest chain 42 peptides. Score 0.608 Round 2: 557 peptides, 43 chains. Longest chain 46 peptides. Score 0.687 Round 3: 555 peptides, 46 chains. Longest chain 38 peptides. Score 0.673 Round 4: 556 peptides, 46 chains. Longest chain 47 peptides. Score 0.674 Round 5: 560 peptides, 44 chains. Longest chain 47 peptides. Score 0.686 Taking the results from Round 2 Chains 52, Residues 514, Estimated correctness of the model 54.5 % 12 chains (237 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8298 restraints for refining 5092 atoms. 5387 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2502 (Rfree = 0.000) for 5092 atoms. Found 34 (34 requested) and removed 47 (19 requested) atoms. Cycle 27: After refmac, R = 0.2362 (Rfree = 0.000) for 5057 atoms. Found 34 (34 requested) and removed 27 (19 requested) atoms. Cycle 28: After refmac, R = 0.2286 (Rfree = 0.000) for 5047 atoms. Found 17 (34 requested) and removed 19 (19 requested) atoms. Cycle 29: After refmac, R = 0.2223 (Rfree = 0.000) for 5033 atoms. Found 12 (34 requested) and removed 23 (19 requested) atoms. Cycle 30: After refmac, R = 0.2178 (Rfree = 0.000) for 5017 atoms. Found 15 (33 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.93 2.28 Search for helices and strands: 0 residues in 0 chains, 5143 seeds are put forward NCS extension: 39 residues added (17 deleted due to clashes), 5182 seeds are put forward Round 1: 520 peptides, 54 chains. Longest chain 25 peptides. Score 0.602 Round 2: 543 peptides, 40 chains. Longest chain 48 peptides. Score 0.688 Round 3: 534 peptides, 42 chains. Longest chain 52 peptides. Score 0.672 Round 4: 531 peptides, 48 chains. Longest chain 29 peptides. Score 0.641 Round 5: 541 peptides, 48 chains. Longest chain 44 peptides. Score 0.651 Taking the results from Round 2 Chains 49, Residues 503, Estimated correctness of the model 54.7 % 11 chains (267 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8025 restraints for refining 5092 atoms. 5041 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2530 (Rfree = 0.000) for 5092 atoms. Found 34 (34 requested) and removed 37 (19 requested) atoms. Cycle 32: After refmac, R = 0.2376 (Rfree = 0.000) for 5059 atoms. Found 34 (34 requested) and removed 28 (19 requested) atoms. Cycle 33: After refmac, R = 0.2260 (Rfree = 0.000) for 5052 atoms. Found 21 (34 requested) and removed 23 (19 requested) atoms. Cycle 34: After refmac, R = 0.2203 (Rfree = 0.000) for 5042 atoms. Found 13 (34 requested) and removed 22 (19 requested) atoms. Cycle 35: After refmac, R = 0.2165 (Rfree = 0.000) for 5030 atoms. Found 19 (33 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.87 2.23 Search for helices and strands: 0 residues in 0 chains, 5161 seeds are put forward NCS extension: 22 residues added (7 deleted due to clashes), 5183 seeds are put forward Round 1: 534 peptides, 53 chains. Longest chain 38 peptides. Score 0.621 Round 2: 538 peptides, 51 chains. Longest chain 36 peptides. Score 0.634 Round 3: 545 peptides, 51 chains. Longest chain 37 peptides. Score 0.641 Round 4: 553 peptides, 50 chains. Longest chain 33 peptides. Score 0.653 Round 5: 523 peptides, 52 chains. Longest chain 31 peptides. Score 0.615 Taking the results from Round 4 Chains 57, Residues 503, Estimated correctness of the model 45.0 % 15 chains (262 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8082 restraints for refining 5092 atoms. 5120 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2576 (Rfree = 0.000) for 5092 atoms. Found 34 (34 requested) and removed 55 (19 requested) atoms. Cycle 37: After refmac, R = 0.2357 (Rfree = 0.000) for 5055 atoms. Found 34 (34 requested) and removed 30 (19 requested) atoms. Cycle 38: After refmac, R = 0.2237 (Rfree = 0.000) for 5050 atoms. Found 18 (34 requested) and removed 26 (19 requested) atoms. Cycle 39: After refmac, R = 0.2183 (Rfree = 0.000) for 5036 atoms. Found 19 (34 requested) and removed 30 (19 requested) atoms. Cycle 40: After refmac, R = 0.2142 (Rfree = 0.000) for 5017 atoms. Found 16 (33 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.90 2.26 Search for helices and strands: 0 residues in 0 chains, 5147 seeds are put forward NCS extension: 18 residues added (14 deleted due to clashes), 5165 seeds are put forward Round 1: 514 peptides, 52 chains. Longest chain 32 peptides. Score 0.605 Round 2: 530 peptides, 49 chains. Longest chain 33 peptides. Score 0.636 Round 3: 535 peptides, 47 chains. Longest chain 36 peptides. Score 0.650 Round 4: 527 peptides, 47 chains. Longest chain 30 peptides. Score 0.642 Round 5: 543 peptides, 50 chains. Longest chain 32 peptides. Score 0.644 Taking the results from Round 3 Chains 55, Residues 488, Estimated correctness of the model 44.1 % 14 chains (234 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8515 restraints for refining 5092 atoms. 5735 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2497 (Rfree = 0.000) for 5092 atoms. Found 34 (34 requested) and removed 42 (19 requested) atoms. Cycle 42: After refmac, R = 0.2327 (Rfree = 0.000) for 5065 atoms. Found 34 (34 requested) and removed 25 (19 requested) atoms. Cycle 43: After refmac, R = 0.2246 (Rfree = 0.000) for 5064 atoms. Found 21 (34 requested) and removed 27 (19 requested) atoms. Cycle 44: After refmac, R = 0.2210 (Rfree = 0.000) for 5053 atoms. Found 18 (34 requested) and removed 26 (19 requested) atoms. Cycle 45: After refmac, R = 0.2180 (Rfree = 0.000) for 5043 atoms. Found 17 (34 requested) and removed 24 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.92 2.27 Search for helices and strands: 0 residues in 0 chains, 5149 seeds are put forward NCS extension: 11 residues added (15 deleted due to clashes), 5160 seeds are put forward Round 1: 524 peptides, 56 chains. Longest chain 33 peptides. Score 0.596 Round 2: 549 peptides, 50 chains. Longest chain 34 peptides. Score 0.649 Round 3: 549 peptides, 49 chains. Longest chain 45 peptides. Score 0.654 Round 4: 563 peptides, 48 chains. Longest chain 32 peptides. Score 0.671 Round 5: 549 peptides, 47 chains. Longest chain 43 peptides. Score 0.663 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 515, Estimated correctness of the model 50.1 % 11 chains (201 residues) have been docked in sequence Sequence coverage is 38 % Consider running further cycles of model building using 2g0t-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 44 A and 56 A Built loop between residues 217 A and 228 A Built loop between residues 238 A and 249 A Built loop between residues 235 B and 243 B 41 chains (533 residues) following loop building 7 chains (239 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17072 reflections ( 99.75 % complete ) and 8263 restraints for refining 5092 atoms. 5362 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2603 (Rfree = 0.000) for 5092 atoms. Found 0 (34 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2496 (Rfree = 0.000) for 5051 atoms. Found 0 (34 requested) and removed 10 (19 requested) atoms. Cycle 48: After refmac, R = 0.2440 (Rfree = 0.000) for 5034 atoms. Found 0 (34 requested) and removed 11 (19 requested) atoms. Cycle 49: After refmac, R = 0.2401 (Rfree = 0.000) for 5017 atoms. Found 0 (33 requested) and removed 5 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:33:09 GMT 2018 Job finished. TimeTaking 190.47 Used memory is bytes: 19522664