null Sun 23 Dec 22:23:07 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2avn-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2avn-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-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/2avn-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-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 22:23:17 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2avn-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 654 and 0 Target number of residues in the AU: 654 Target solvent content: 0.6367 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-3.4-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: 181 Cell parameters: 133.767 133.767 188.622 90.000 90.000 120.000 Input sequence file: 2avn-3.4-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 3.400 Wilson plot Bfac: 70.16 14269 reflections ( 99.68 % complete ) and 0 restraints for refining 4645 atoms. Observations/parameters ratio is 0.77 ------------------------------------------------------ Starting model: R = 0.3533 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3071 (Rfree = 0.000) for 4645 atoms. Found 35 (35 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 2.46 Search for helices and strands: 0 residues in 0 chains, 4743 seeds are put forward NCS extension: 0 residues added, 4743 seeds are put forward Round 1: 351 peptides, 45 chains. Longest chain 23 peptides. Score 0.488 Round 2: 401 peptides, 41 chains. Longest chain 34 peptides. Score 0.585 Round 3: 399 peptides, 36 chains. Longest chain 32 peptides. Score 0.613 Round 4: 394 peptides, 33 chains. Longest chain 34 peptides. Score 0.625 Round 5: 402 peptides, 36 chains. Longest chain 27 peptides. Score 0.617 Taking the results from Round 4 Chains 35, Residues 361, Estimated correctness of the model 36.6 % 6 chains (121 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7443 restraints for refining 4151 atoms. 5507 conditional restraints added. Observations/parameters ratio is 0.86 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2813 (Rfree = 0.000) for 4151 atoms. Found 31 (31 requested) and removed 23 (15 requested) atoms. Cycle 2: After refmac, R = 0.2580 (Rfree = 0.000) for 4096 atoms. Found 26 (31 requested) and removed 25 (15 requested) atoms. Cycle 3: After refmac, R = 0.2433 (Rfree = 0.000) for 4073 atoms. Found 17 (30 requested) and removed 19 (15 requested) atoms. Cycle 4: After refmac, R = 0.2376 (Rfree = 0.000) for 4047 atoms. Found 19 (30 requested) and removed 19 (15 requested) atoms. Cycle 5: After refmac, R = 0.2318 (Rfree = 0.000) for 4032 atoms. Found 13 (30 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 2.45 Search for helices and strands: 0 residues in 0 chains, 4170 seeds are put forward NCS extension: 25 residues added (27 deleted due to clashes), 4195 seeds are put forward Round 1: 397 peptides, 32 chains. Longest chain 46 peptides. Score 0.635 Round 2: 405 peptides, 33 chains. Longest chain 32 peptides. Score 0.638 Round 3: 412 peptides, 33 chains. Longest chain 37 peptides. Score 0.646 Round 4: 408 peptides, 34 chains. Longest chain 25 peptides. Score 0.636 Round 5: 394 peptides, 37 chains. Longest chain 26 peptides. Score 0.601 Taking the results from Round 3 Chains 35, Residues 379, Estimated correctness of the model 43.0 % 4 chains (105 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7017 restraints for refining 3938 atoms. 5090 conditional restraints added. Observations/parameters ratio is 0.91 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2625 (Rfree = 0.000) for 3938 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. Cycle 7: After refmac, R = 0.2401 (Rfree = 0.000) for 3908 atoms. Found 24 (29 requested) and removed 16 (14 requested) atoms. Cycle 8: After refmac, R = 0.2348 (Rfree = 0.000) for 3894 atoms. Found 11 (29 requested) and removed 16 (14 requested) atoms. Cycle 9: After refmac, R = 0.2263 (Rfree = 0.000) for 3878 atoms. Found 6 (29 requested) and removed 16 (14 requested) atoms. Cycle 10: After refmac, R = 0.2205 (Rfree = 0.000) for 3860 atoms. Found 6 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 2.46 Search for helices and strands: 0 residues in 0 chains, 4008 seeds are put forward NCS extension: 36 residues added (9 deleted due to clashes), 4044 seeds are put forward Round 1: 381 peptides, 39 chains. Longest chain 27 peptides. Score 0.571 Round 2: 396 peptides, 39 chains. Longest chain 24 peptides. Score 0.591 Round 3: 410 peptides, 38 chains. Longest chain 34 peptides. Score 0.615 Round 4: 411 peptides, 33 chains. Longest chain 51 peptides. Score 0.645 Round 5: 407 peptides, 36 chains. Longest chain 30 peptides. Score 0.623 Taking the results from Round 4 Chains 33, Residues 378, Estimated correctness of the model 42.7 % 4 chains (95 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7237 restraints for refining 3941 atoms. 5354 conditional restraints added. Observations/parameters ratio is 0.91 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2634 (Rfree = 0.000) for 3941 atoms. Found 29 (29 requested) and removed 25 (14 requested) atoms. Cycle 12: After refmac, R = 0.2435 (Rfree = 0.000) for 3926 atoms. Found 27 (29 requested) and removed 18 (14 requested) atoms. Cycle 13: After refmac, R = 0.2339 (Rfree = 0.000) for 3924 atoms. Found 22 (29 requested) and removed 15 (14 requested) atoms. Cycle 14: After refmac, R = 0.2267 (Rfree = 0.000) for 3922 atoms. Found 10 (29 requested) and removed 14 (14 requested) atoms. Cycle 15: After refmac, R = 0.2264 (Rfree = 0.000) for 3910 atoms. Found 14 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 2.46 Search for helices and strands: 0 residues in 0 chains, 4037 seeds are put forward NCS extension: 35 residues added (8 deleted due to clashes), 4072 seeds are put forward Round 1: 382 peptides, 35 chains. Longest chain 30 peptides. Score 0.598 Round 2: 406 peptides, 39 chains. Longest chain 22 peptides. Score 0.604 Round 3: 394 peptides, 37 chains. Longest chain 26 peptides. Score 0.601 Round 4: 388 peptides, 39 chains. Longest chain 31 peptides. Score 0.581 Round 5: 382 peptides, 36 chains. Longest chain 42 peptides. Score 0.592 Taking the results from Round 2 Chains 39, Residues 367, Estimated correctness of the model 30.0 % 3 chains (34 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7537 restraints for refining 3810 atoms. 5967 conditional restraints added. Observations/parameters ratio is 0.94 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2541 (Rfree = 0.000) for 3810 atoms. Found 28 (28 requested) and removed 16 (14 requested) atoms. Cycle 17: After refmac, R = 0.2297 (Rfree = 0.000) for 3806 atoms. Found 17 (28 requested) and removed 15 (14 requested) atoms. Cycle 18: After refmac, R = 0.2201 (Rfree = 0.000) for 3802 atoms. Found 8 (28 requested) and removed 14 (14 requested) atoms. Cycle 19: After refmac, R = 0.2182 (Rfree = 0.000) for 3791 atoms. Found 16 (28 requested) and removed 15 (14 requested) atoms. Cycle 20: After refmac, R = 0.2133 (Rfree = 0.000) for 3790 atoms. Found 8 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.35 2.49 Search for helices and strands: 0 residues in 0 chains, 3903 seeds are put forward NCS extension: 13 residues added (11 deleted due to clashes), 3916 seeds are put forward Round 1: 406 peptides, 43 chains. Longest chain 25 peptides. Score 0.579 Round 2: 413 peptides, 36 chains. Longest chain 31 peptides. Score 0.630 Round 3: 409 peptides, 39 chains. Longest chain 31 peptides. Score 0.608 Round 4: 399 peptides, 40 chains. Longest chain 27 peptides. Score 0.589 Round 5: 393 peptides, 35 chains. Longest chain 29 peptides. Score 0.612 Taking the results from Round 2 Chains 40, Residues 377, Estimated correctness of the model 38.2 % 4 chains (95 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 6863 restraints for refining 3802 atoms. 4998 conditional restraints added. Observations/parameters ratio is 0.94 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2489 (Rfree = 0.000) for 3802 atoms. Found 28 (28 requested) and removed 23 (14 requested) atoms. Cycle 22: After refmac, R = 0.2351 (Rfree = 0.000) for 3790 atoms. Found 28 (28 requested) and removed 16 (14 requested) atoms. Cycle 23: After refmac, R = 0.2280 (Rfree = 0.000) for 3794 atoms. Found 28 (28 requested) and removed 15 (14 requested) atoms. Cycle 24: After refmac, R = 0.2326 (Rfree = 0.000) for 3801 atoms. Found 19 (28 requested) and removed 16 (14 requested) atoms. Cycle 25: After refmac, R = 0.2122 (Rfree = 0.000) for 3796 atoms. Found 17 (28 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.35 2.49 Search for helices and strands: 0 residues in 0 chains, 3936 seeds are put forward NCS extension: 34 residues added (7 deleted due to clashes), 3970 seeds are put forward Round 1: 405 peptides, 39 chains. Longest chain 51 peptides. Score 0.603 Round 2: 405 peptides, 35 chains. Longest chain 43 peptides. Score 0.627 Round 3: 413 peptides, 37 chains. Longest chain 41 peptides. Score 0.624 Round 4: 409 peptides, 35 chains. Longest chain 34 peptides. Score 0.631 Round 5: 406 peptides, 32 chains. Longest chain 30 peptides. Score 0.645 Taking the results from Round 5 Chains 34, Residues 374, Estimated correctness of the model 42.7 % 3 chains (75 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 7486 restraints for refining 3944 atoms. 5650 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2548 (Rfree = 0.000) for 3944 atoms. Found 29 (29 requested) and removed 20 (14 requested) atoms. Cycle 27: After refmac, R = 0.2306 (Rfree = 0.000) for 3938 atoms. Found 22 (29 requested) and removed 16 (14 requested) atoms. Cycle 28: After refmac, R = 0.2187 (Rfree = 0.000) for 3933 atoms. Found 8 (29 requested) and removed 15 (14 requested) atoms. Cycle 29: After refmac, R = 0.2135 (Rfree = 0.000) for 3922 atoms. Found 10 (29 requested) and removed 14 (14 requested) atoms. Cycle 30: After refmac, R = 0.2093 (Rfree = 0.000) for 3916 atoms. Found 16 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.33 2.47 Search for helices and strands: 0 residues in 0 chains, 4077 seeds are put forward NCS extension: 8 residues added (10 deleted due to clashes), 4085 seeds are put forward Round 1: 397 peptides, 39 chains. Longest chain 31 peptides. Score 0.592 Round 2: 406 peptides, 36 chains. Longest chain 35 peptides. Score 0.622 Round 3: 418 peptides, 31 chains. Longest chain 50 peptides. Score 0.665 Round 4: 401 peptides, 38 chains. Longest chain 28 peptides. Score 0.604 Round 5: 421 peptides, 38 chains. Longest chain 35 peptides. Score 0.628 Taking the results from Round 3 Chains 34, Residues 387, Estimated correctness of the model 48.4 % 5 chains (153 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 6978 restraints for refining 4023 atoms. 4807 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2592 (Rfree = 0.000) for 4023 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. Cycle 32: After refmac, R = 0.2359 (Rfree = 0.000) for 4017 atoms. Found 19 (30 requested) and removed 15 (15 requested) atoms. Cycle 33: After refmac, R = 0.2409 (Rfree = 0.000) for 4007 atoms. Found 29 (30 requested) and removed 19 (15 requested) atoms. Cycle 34: After refmac, R = 0.2177 (Rfree = 0.000) for 4003 atoms. Found 17 (30 requested) and removed 19 (15 requested) atoms. Cycle 35: After refmac, R = 0.2083 (Rfree = 0.000) for 3990 atoms. Found 13 (30 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 2.49 Search for helices and strands: 0 residues in 0 chains, 4104 seeds are put forward NCS extension: 45 residues added (16 deleted due to clashes), 4149 seeds are put forward Round 1: 408 peptides, 35 chains. Longest chain 32 peptides. Score 0.630 Round 2: 432 peptides, 31 chains. Longest chain 50 peptides. Score 0.680 Round 3: 431 peptides, 39 chains. Longest chain 34 peptides. Score 0.634 Round 4: 426 peptides, 35 chains. Longest chain 35 peptides. Score 0.651 Round 5: 416 peptides, 38 chains. Longest chain 30 peptides. Score 0.622 Taking the results from Round 2 Chains 36, Residues 401, Estimated correctness of the model 52.6 % 8 chains (168 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 6627 restraints for refining 4008 atoms. 4287 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2495 (Rfree = 0.000) for 4008 atoms. Found 30 (30 requested) and removed 30 (15 requested) atoms. Cycle 37: After refmac, R = 0.2266 (Rfree = 0.000) for 3996 atoms. Found 15 (30 requested) and removed 19 (15 requested) atoms. Cycle 38: After refmac, R = 0.2194 (Rfree = 0.000) for 3982 atoms. Found 21 (30 requested) and removed 18 (15 requested) atoms. Cycle 39: After refmac, R = 0.2120 (Rfree = 0.000) for 3965 atoms. Found 9 (30 requested) and removed 16 (15 requested) atoms. Cycle 40: After refmac, R = 0.2059 (Rfree = 0.000) for 3948 atoms. Found 7 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.34 2.48 Search for helices and strands: 0 residues in 0 chains, 4045 seeds are put forward NCS extension: 32 residues added (10 deleted due to clashes), 4077 seeds are put forward Round 1: 401 peptides, 34 chains. Longest chain 36 peptides. Score 0.628 Round 2: 405 peptides, 26 chains. Longest chain 45 peptides. Score 0.678 Round 3: 411 peptides, 33 chains. Longest chain 31 peptides. Score 0.645 Round 4: 411 peptides, 33 chains. Longest chain 29 peptides. Score 0.645 Round 5: 428 peptides, 34 chains. Longest chain 42 peptides. Score 0.659 Taking the results from Round 2 Chains 27, Residues 379, Estimated correctness of the model 52.0 % 6 chains (192 residues) have been docked in sequence ------------------------------------------------------ 14269 reflections ( 99.68 % complete ) and 6606 restraints for refining 4008 atoms. 4274 conditional restraints added. Observations/parameters ratio is 0.89 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2446 (Rfree = 0.000) for 4008 atoms. Found 30 (30 requested) and removed 24 (15 requested) atoms. Cycle 42: After refmac, R = 0.2209 (Rfree = 0.000) for 3996 atoms. Found 24 (30 requested) and removed 20 (15 requested) atoms. Cycle 43: After refmac, R = 0.2131 (Rfree = 0.000) for 3987 atoms. Found 11 (30 requested) and removed 16 (15 requested) atoms. Cycle 44: After refmac, R = 0.2130 (Rfree = 0.000) for 3978 atoms. Found 14 (30 requested) and removed 15 (15 requested) atoms. Cycle 45: After refmac, R = 0.2113 (Rfree = 0.000) for 3974 atoms. Found 15 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 2.47 Search for helices and strands: 0 residues in 0 chains, 4093 seeds are put forward NCS extension: 32 residues added (17 deleted due to clashes), 4125 seeds are put forward Round 1: 392 peptides, 41 chains. Longest chain 36 peptides. Score 0.573 Round 2: 403 peptides, 31 chains. Longest chain 43 peptides. Score 0.648 Round 3: 415 peptides, 36 chains. Longest chain 35 peptides. Score 0.633 Round 4: 407 peptides, 32 chains. Longest chain 43 peptides. Score 0.646 Round 5: 423 peptides, 30 chains. Longest chain 47 peptides. Score 0.676 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 393, Estimated correctness of the model 51.5 % 7 chains (164 residues) have been docked in sequence Sequence coverage is 41 % Consider running further cycles of model building using 2avn-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 194 B and 197 B Built loop between residues 220 B and 234 B 29 chains (401 residues) following loop building 5 chains (179 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14269 reflections ( 99.68 % complete ) and 6712 restraints for refining 4039 atoms. 4418 conditional restraints added. Observations/parameters ratio is 0.88 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2579 (Rfree = 0.000) for 4039 atoms. Found 0 (30 requested) and removed 14 (15 requested) atoms. Cycle 47: After refmac, R = 0.2383 (Rfree = 0.000) for 4010 atoms. Found 0 (30 requested) and removed 6 (15 requested) atoms. Cycle 48: After refmac, R = 0.2279 (Rfree = 0.000) for 4001 atoms. Found 0 (30 requested) and removed 8 (15 requested) atoms. Cycle 49: After refmac, R = 0.2374 (Rfree = 0.000) for 3989 atoms. Found 0 (30 requested) and removed 7 (15 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:42:29 GMT 2018 Job finished. TimeTaking 79.36 Used memory is bytes: 18884152