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 2avn-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2avn-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2avn-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-3.2-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/2avn-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-3.2-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/2avn-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-3.2-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 678 and 0 Target number of residues in the AU: 678 Target solvent content: 0.6234 Checking the provided sequence file Detected sequence length: 260 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 520 Adjusted target solvent content: 0.71 Input MTZ file: 2avn-3.2-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: 181 Cell parameters: 133.767 133.767 188.622 90.000 90.000 120.000 Input sequence file: 2avn-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 4160 target number of atoms Had to go as low as 1.15 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: 115.845 3.200 Wilson plot Bfac: 63.12 17047 reflections ( 99.73 % complete ) and 0 restraints for refining 4640 atoms. Observations/parameters ratio is 0.92 ------------------------------------------------------ Starting model: R = 0.3469 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3301 (Rfree = 0.000) for 4640 atoms. Found 41 (41 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 2.40 Search for helices and strands: 0 residues in 0 chains, 4766 seeds are put forward NCS extension: 0 residues added, 4766 seeds are put forward Round 1: 340 peptides, 44 chains. Longest chain 23 peptides. Score 0.478 Round 2: 394 peptides, 42 chains. Longest chain 28 peptides. Score 0.570 Round 3: 417 peptides, 34 chains. Longest chain 48 peptides. Score 0.646 Round 4: 401 peptides, 30 chains. Longest chain 37 peptides. Score 0.651 Round 5: 407 peptides, 33 chains. Longest chain 49 peptides. Score 0.641 Taking the results from Round 4 Chains 32, Residues 371, Estimated correctness of the model 54.1 % 4 chains (96 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 7448 restraints for refining 4072 atoms. 5599 conditional restraints added. Observations/parameters ratio is 1.05 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2913 (Rfree = 0.000) for 4072 atoms. Found 36 (36 requested) and removed 28 (18 requested) atoms. Cycle 2: After refmac, R = 0.2770 (Rfree = 0.000) for 4044 atoms. Found 36 (36 requested) and removed 20 (18 requested) atoms. Cycle 3: After refmac, R = 0.2740 (Rfree = 0.000) for 4039 atoms. Found 33 (36 requested) and removed 23 (18 requested) atoms. Cycle 4: After refmac, R = 0.2690 (Rfree = 0.000) for 4034 atoms. Found 31 (36 requested) and removed 22 (18 requested) atoms. Cycle 5: After refmac, R = 0.2592 (Rfree = 0.000) for 4033 atoms. Found 17 (36 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 2.45 Search for helices and strands: 0 residues in 0 chains, 4201 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 4231 seeds are put forward Round 1: 402 peptides, 35 chains. Longest chain 38 peptides. Score 0.623 Round 2: 424 peptides, 31 chains. Longest chain 40 peptides. Score 0.671 Round 3: 405 peptides, 30 chains. Longest chain 36 peptides. Score 0.656 Round 4: 419 peptides, 34 chains. Longest chain 43 peptides. Score 0.649 Round 5: 433 peptides, 32 chains. Longest chain 38 peptides. Score 0.675 Taking the results from Round 5 Chains 35, Residues 401, Estimated correctness of the model 59.7 % 11 chains (205 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 6597 restraints for refining 4183 atoms. 4137 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2922 (Rfree = 0.000) for 4183 atoms. Found 37 (37 requested) and removed 41 (18 requested) atoms. Cycle 7: After refmac, R = 0.2733 (Rfree = 0.000) for 4131 atoms. Found 28 (37 requested) and removed 21 (18 requested) atoms. Cycle 8: After refmac, R = 0.2620 (Rfree = 0.000) for 4109 atoms. Found 24 (37 requested) and removed 23 (18 requested) atoms. Cycle 9: After refmac, R = 0.2512 (Rfree = 0.000) for 4099 atoms. Found 17 (36 requested) and removed 18 (18 requested) atoms. Cycle 10: After refmac, R = 0.2475 (Rfree = 0.000) for 4089 atoms. Found 14 (36 requested) and removed 18 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 2.43 Search for helices and strands: 0 residues in 0 chains, 4229 seeds are put forward NCS extension: 31 residues added (13 deleted due to clashes), 4260 seeds are put forward Round 1: 419 peptides, 38 chains. Longest chain 34 peptides. Score 0.626 Round 2: 429 peptides, 29 chains. Longest chain 51 peptides. Score 0.687 Round 3: 424 peptides, 32 chains. Longest chain 39 peptides. Score 0.666 Round 4: 431 peptides, 29 chains. Longest chain 58 peptides. Score 0.689 Round 5: 425 peptides, 33 chains. Longest chain 37 peptides. Score 0.661 Taking the results from Round 4 Chains 35, Residues 402, Estimated correctness of the model 62.8 % 11 chains (232 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 6570 restraints for refining 4236 atoms. 3996 conditional restraints added. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2849 (Rfree = 0.000) for 4236 atoms. Found 38 (38 requested) and removed 31 (19 requested) atoms. Cycle 12: After refmac, R = 0.2666 (Rfree = 0.000) for 4206 atoms. Found 36 (38 requested) and removed 26 (19 requested) atoms. Cycle 13: After refmac, R = 0.2649 (Rfree = 0.000) for 4190 atoms. Found 35 (37 requested) and removed 19 (18 requested) atoms. Cycle 14: After refmac, R = 0.2565 (Rfree = 0.000) for 4193 atoms. Found 35 (37 requested) and removed 22 (18 requested) atoms. Cycle 15: After refmac, R = 0.2379 (Rfree = 0.000) for 4191 atoms. Found 23 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 2.40 Search for helices and strands: 0 residues in 0 chains, 4313 seeds are put forward NCS extension: 11 residues added (14 deleted due to clashes), 4324 seeds are put forward Round 1: 392 peptides, 34 chains. Longest chain 34 peptides. Score 0.617 Round 2: 431 peptides, 38 chains. Longest chain 34 peptides. Score 0.640 Round 3: 408 peptides, 31 chains. Longest chain 46 peptides. Score 0.653 Round 4: 420 peptides, 35 chains. Longest chain 33 peptides. Score 0.644 Round 5: 415 peptides, 31 chains. Longest chain 42 peptides. Score 0.661 Taking the results from Round 5 Chains 35, Residues 384, Estimated correctness of the model 56.5 % 6 chains (137 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 7558 restraints for refining 4210 atoms. 5429 conditional restraints added. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2854 (Rfree = 0.000) for 4210 atoms. Found 37 (37 requested) and removed 37 (18 requested) atoms. Cycle 17: After refmac, R = 0.2638 (Rfree = 0.000) for 4173 atoms. Found 37 (37 requested) and removed 22 (18 requested) atoms. Cycle 18: After refmac, R = 0.2548 (Rfree = 0.000) for 4171 atoms. Found 24 (37 requested) and removed 20 (18 requested) atoms. Cycle 19: After refmac, R = 0.2608 (Rfree = 0.000) for 4163 atoms. Found 37 (37 requested) and removed 21 (18 requested) atoms. Cycle 20: After refmac, R = 0.2466 (Rfree = 0.000) for 4165 atoms. Found 21 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 2.41 Search for helices and strands: 0 residues in 0 chains, 4308 seeds are put forward NCS extension: 12 residues added (15 deleted due to clashes), 4320 seeds are put forward Round 1: 396 peptides, 34 chains. Longest chain 31 peptides. Score 0.622 Round 2: 417 peptides, 29 chains. Longest chain 45 peptides. Score 0.675 Round 3: 422 peptides, 32 chains. Longest chain 45 peptides. Score 0.663 Round 4: 431 peptides, 30 chains. Longest chain 41 peptides. Score 0.684 Round 5: 436 peptides, 34 chains. Longest chain 42 peptides. Score 0.668 Taking the results from Round 4 Chains 35, Residues 401, Estimated correctness of the model 61.7 % 8 chains (187 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 6889 restraints for refining 4197 atoms. 4476 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2804 (Rfree = 0.000) for 4197 atoms. Found 36 (37 requested) and removed 39 (18 requested) atoms. Cycle 22: After refmac, R = 0.2580 (Rfree = 0.000) for 4156 atoms. Found 26 (37 requested) and removed 27 (18 requested) atoms. Cycle 23: After refmac, R = 0.2439 (Rfree = 0.000) for 4124 atoms. Found 27 (37 requested) and removed 21 (18 requested) atoms. Cycle 24: After refmac, R = 0.2334 (Rfree = 0.000) for 4109 atoms. Found 19 (37 requested) and removed 23 (18 requested) atoms. Cycle 25: After refmac, R = 0.2290 (Rfree = 0.000) for 4082 atoms. Found 15 (36 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 2.40 Search for helices and strands: 0 residues in 0 chains, 4172 seeds are put forward NCS extension: 9 residues added (29 deleted due to clashes), 4181 seeds are put forward Round 1: 419 peptides, 30 chains. Longest chain 40 peptides. Score 0.671 Round 2: 408 peptides, 29 chains. Longest chain 50 peptides. Score 0.665 Round 3: 416 peptides, 28 chains. Longest chain 51 peptides. Score 0.679 Round 4: 434 peptides, 29 chains. Longest chain 43 peptides. Score 0.693 Round 5: 427 peptides, 32 chains. Longest chain 41 peptides. Score 0.669 Taking the results from Round 4 Chains 34, Residues 405, Estimated correctness of the model 63.7 % 9 chains (229 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 6393 restraints for refining 4206 atoms. 3759 conditional restraints added. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2687 (Rfree = 0.000) for 4206 atoms. Found 37 (37 requested) and removed 36 (18 requested) atoms. Cycle 27: After refmac, R = 0.2530 (Rfree = 0.000) for 4182 atoms. Found 37 (37 requested) and removed 32 (18 requested) atoms. Cycle 28: After refmac, R = 0.2584 (Rfree = 0.000) for 4165 atoms. Found 37 (37 requested) and removed 24 (18 requested) atoms. Cycle 29: After refmac, R = 0.2233 (Rfree = 0.000) for 4165 atoms. Found 33 (37 requested) and removed 23 (18 requested) atoms. Cycle 30: After refmac, R = 0.2440 (Rfree = 0.000) for 4163 atoms. Found 37 (37 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 2.37 Search for helices and strands: 0 residues in 0 chains, 4305 seeds are put forward NCS extension: 7 residues added (12 deleted due to clashes), 4312 seeds are put forward Round 1: 426 peptides, 34 chains. Longest chain 45 peptides. Score 0.657 Round 2: 431 peptides, 31 chains. Longest chain 38 peptides. Score 0.679 Round 3: 423 peptides, 24 chains. Longest chain 49 peptides. Score 0.708 Round 4: 435 peptides, 29 chains. Longest chain 37 peptides. Score 0.694 Round 5: 420 peptides, 28 chains. Longest chain 40 peptides. Score 0.683 Taking the results from Round 3 Chains 26, Residues 399, Estimated correctness of the model 66.9 % 11 chains (275 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 63 A and 68 A Built loop between residues 138 B and 144 B 24 chains (408 residues) following loop building 9 chains (284 residues) in sequence following loop building ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 6227 restraints for refining 4324 atoms. 3341 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2729 (Rfree = 0.000) for 4324 atoms. Found 38 (38 requested) and removed 26 (19 requested) atoms. Cycle 32: After refmac, R = 0.2676 (Rfree = 0.000) for 4316 atoms. Found 37 (37 requested) and removed 34 (19 requested) atoms. Cycle 33: After refmac, R = 0.2701 (Rfree = 0.000) for 4297 atoms. Found 36 (36 requested) and removed 33 (19 requested) atoms. Cycle 34: After refmac, R = 0.2472 (Rfree = 0.000) for 4284 atoms. Found 32 (36 requested) and removed 28 (19 requested) atoms. Cycle 35: After refmac, R = 0.2231 (Rfree = 0.000) for 4277 atoms. Found 23 (35 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 2.37 Search for helices and strands: 0 residues in 0 chains, 4388 seeds are put forward NCS extension: 43 residues added (19 deleted due to clashes), 4431 seeds are put forward Round 1: 419 peptides, 32 chains. Longest chain 41 peptides. Score 0.660 Round 2: 442 peptides, 34 chains. Longest chain 59 peptides. Score 0.674 Round 3: 450 peptides, 29 chains. Longest chain 37 peptides. Score 0.709 Round 4: 429 peptides, 32 chains. Longest chain 50 peptides. Score 0.671 Round 5: 421 peptides, 36 chains. Longest chain 31 peptides. Score 0.640 Taking the results from Round 3 Chains 35, Residues 421, Estimated correctness of the model 67.1 % 12 chains (253 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 A and 71 A 34 chains (424 residues) following loop building 11 chains (261 residues) in sequence following loop building ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 6295 restraints for refining 4293 atoms. 3483 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2699 (Rfree = 0.000) for 4293 atoms. Found 34 (34 requested) and removed 29 (19 requested) atoms. Cycle 37: After refmac, R = 0.2522 (Rfree = 0.000) for 4276 atoms. Found 33 (33 requested) and removed 36 (19 requested) atoms. Cycle 38: After refmac, R = 0.2258 (Rfree = 0.000) for 4254 atoms. Found 33 (33 requested) and removed 31 (19 requested) atoms. Cycle 39: After refmac, R = 0.2103 (Rfree = 0.000) for 4249 atoms. Found 27 (32 requested) and removed 24 (19 requested) atoms. Cycle 40: After refmac, R = 0.2035 (Rfree = 0.000) for 4245 atoms. Found 25 (31 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 2.36 Search for helices and strands: 0 residues in 0 chains, 4377 seeds are put forward NCS extension: 32 residues added (37 deleted due to clashes), 4409 seeds are put forward Round 1: 432 peptides, 31 chains. Longest chain 51 peptides. Score 0.680 Round 2: 413 peptides, 26 chains. Longest chain 36 peptides. Score 0.687 Round 3: 423 peptides, 35 chains. Longest chain 25 peptides. Score 0.648 Round 4: 417 peptides, 32 chains. Longest chain 36 peptides. Score 0.658 Round 5: 428 peptides, 33 chains. Longest chain 33 peptides. Score 0.665 Taking the results from Round 2 Chains 32, Residues 387, Estimated correctness of the model 62.4 % 11 chains (215 residues) have been docked in sequence ------------------------------------------------------ 17047 reflections ( 99.73 % complete ) and 6786 restraints for refining 4167 atoms. 4303 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2487 (Rfree = 0.000) for 4167 atoms. Found 30 (30 requested) and removed 30 (18 requested) atoms. Cycle 42: After refmac, R = 0.2302 (Rfree = 0.000) for 4145 atoms. Found 30 (30 requested) and removed 22 (18 requested) atoms. Cycle 43: After refmac, R = 0.2515 (Rfree = 0.000) for 4135 atoms. Found 30 (30 requested) and removed 21 (18 requested) atoms. Cycle 44: After refmac, R = 0.2170 (Rfree = 0.000) for 4129 atoms. Found 30 (30 requested) and removed 25 (18 requested) atoms. Cycle 45: After refmac, R = 0.2203 (Rfree = 0.000) for 4129 atoms. Found 30 (30 requested) and removed 24 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.17 2.35 Search for helices and strands: 0 residues in 0 chains, 4253 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 4274 seeds are put forward Round 1: 416 peptides, 29 chains. Longest chain 48 peptides. Score 0.673 Round 2: 440 peptides, 26 chains. Longest chain 57 peptides. Score 0.714 Round 3: 443 peptides, 30 chains. Longest chain 33 peptides. Score 0.697 Round 4: 425 peptides, 26 chains. Longest chain 39 peptides. Score 0.699 Round 5: 421 peptides, 31 chains. Longest chain 33 peptides. Score 0.668 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 414, Estimated correctness of the model 68.1 % 13 chains (271 residues) have been docked in sequence Sequence coverage is 65 % Consider running further cycles of model building using 2avn-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 204 A and 208 A Built loop between residues 103 B and 109 B Built loop between residues 137 B and 144 B 29 chains (427 residues) following loop building 10 chains (285 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17047 reflections ( 99.73 % complete ) and 6069 restraints for refining 4212 atoms. 3160 conditional restraints added. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2460 (Rfree = 0.000) for 4212 atoms. Found 0 (30 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2386 (Rfree = 0.000) for 4160 atoms. Found 0 (29 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2184 (Rfree = 0.000) for 4124 atoms. Found 0 (28 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2065 (Rfree = 0.000) for 4092 atoms. Found 0 (27 requested) and removed 8 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:45:51 GMT 2018 Job finished. TimeTaking 82.87 Used memory is bytes: 17847872