Mon 24 Dec 00:12:47 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2f4p-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2f4p-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2f4p-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-4.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-4.0-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 00:12:51 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/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-4.0-parrot-mrncs/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 367 and 0 Target number of residues in the AU: 367 Target solvent content: 0.6456 Checking the provided sequence file Detected sequence length: 147 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 588 Adjusted target solvent content: 0.43 Input MTZ file: 2f4p-4.0-parrot-mrncs.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: 170 Cell parameters: 71.746 71.746 188.600 90.000 90.000 120.000 Input sequence file: 2f4p-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4704 target number of atoms Had to go as low as 0.65 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: 21.543 4.001 Wilson plot Bfac: 75.05 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4616 reflections ( 99.29 % complete ) and 0 restraints for refining 5198 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3450 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3453 (Rfree = 0.000) for 5198 atoms. Found 24 (24 requested) and removed 232 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.88 4.26 Search for helices and strands: 0 residues in 0 chains, 5038 seeds are put forward NCS extension: 0 residues added, 5038 seeds are put forward Round 1: 132 peptides, 29 chains. Longest chain 8 peptides. Score 0.228 Round 2: 183 peptides, 39 chains. Longest chain 8 peptides. Score 0.260 Round 3: 205 peptides, 42 chains. Longest chain 8 peptides. Score 0.291 Round 4: 208 peptides, 34 chains. Longest chain 21 peptides. Score 0.404 Round 5: 213 peptides, 35 chains. Longest chain 12 peptides. Score 0.406 Taking the results from Round 5 Chains 35, Residues 178, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 10493 restraints for refining 4246 atoms. 9805 conditional restraints added. Observations/parameters ratio is 0.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3126 (Rfree = 0.000) for 4246 atoms. Found 20 (20 requested) and removed 94 (10 requested) atoms. Cycle 2: After refmac, R = 0.3026 (Rfree = 0.000) for 4094 atoms. Found 19 (19 requested) and removed 60 (9 requested) atoms. Cycle 3: After refmac, R = 0.2794 (Rfree = 0.000) for 4000 atoms. Found 19 (19 requested) and removed 38 (9 requested) atoms. Cycle 4: After refmac, R = 0.2988 (Rfree = 0.000) for 3939 atoms. Found 18 (18 requested) and removed 51 (9 requested) atoms. Cycle 5: After refmac, R = 0.2925 (Rfree = 0.000) for 3868 atoms. Found 18 (18 requested) and removed 35 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 4.08 Search for helices and strands: 0 residues in 0 chains, 3935 seeds are put forward NCS extension: 11 residues added (3 deleted due to clashes), 3946 seeds are put forward Round 1: 153 peptides, 35 chains. Longest chain 7 peptides. Score 0.214 Round 2: 212 peptides, 41 chains. Longest chain 12 peptides. Score 0.326 Round 3: 213 peptides, 38 chains. Longest chain 11 peptides. Score 0.368 Round 4: 242 peptides, 43 chains. Longest chain 12 peptides. Score 0.390 Round 5: 256 peptides, 42 chains. Longest chain 19 peptides. Score 0.441 Taking the results from Round 5 Chains 43, Residues 214, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 8415 restraints for refining 3754 atoms. 7555 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2972 (Rfree = 0.000) for 3754 atoms. Found 17 (17 requested) and removed 72 (8 requested) atoms. Cycle 7: After refmac, R = 0.2815 (Rfree = 0.000) for 3659 atoms. Found 17 (17 requested) and removed 52 (8 requested) atoms. Cycle 8: After refmac, R = 0.2785 (Rfree = 0.000) for 3585 atoms. Found 17 (17 requested) and removed 51 (8 requested) atoms. Cycle 9: After refmac, R = 0.2310 (Rfree = 0.000) for 3521 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 10: After refmac, R = 0.2669 (Rfree = 0.000) for 3492 atoms. Found 16 (16 requested) and removed 26 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.66 4.02 Search for helices and strands: 0 residues in 0 chains, 3578 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3600 seeds are put forward Round 1: 192 peptides, 42 chains. Longest chain 9 peptides. Score 0.249 Round 2: 212 peptides, 37 chains. Longest chain 14 peptides. Score 0.378 Round 3: 216 peptides, 39 chains. Longest chain 15 peptides. Score 0.364 Round 4: 224 peptides, 39 chains. Longest chain 15 peptides. Score 0.387 Round 5: 225 peptides, 37 chains. Longest chain 18 peptides. Score 0.415 Taking the results from Round 5 Chains 37, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 8714 restraints for refining 3759 atoms. 7999 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2887 (Rfree = 0.000) for 3759 atoms. Found 17 (17 requested) and removed 71 (8 requested) atoms. Cycle 12: After refmac, R = 0.2825 (Rfree = 0.000) for 3670 atoms. Found 17 (17 requested) and removed 34 (8 requested) atoms. Cycle 13: After refmac, R = 0.2858 (Rfree = 0.000) for 3615 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 14: After refmac, R = 0.2809 (Rfree = 0.000) for 3575 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 15: After refmac, R = 0.2381 (Rfree = 0.000) for 3537 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.94 Search for helices and strands: 0 residues in 0 chains, 3614 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3630 seeds are put forward Round 1: 183 peptides, 39 chains. Longest chain 9 peptides. Score 0.260 Round 2: 202 peptides, 40 chains. Longest chain 10 peptides. Score 0.308 Round 3: 215 peptides, 41 chains. Longest chain 12 peptides. Score 0.335 Round 4: 212 peptides, 41 chains. Longest chain 10 peptides. Score 0.326 Round 5: 221 peptides, 41 chains. Longest chain 12 peptides. Score 0.353 Taking the results from Round 5 Chains 41, Residues 180, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 8326 restraints for refining 3665 atoms. 7628 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2915 (Rfree = 0.000) for 3665 atoms. Found 17 (17 requested) and removed 58 (8 requested) atoms. Cycle 17: After refmac, R = 0.2729 (Rfree = 0.000) for 3576 atoms. Found 17 (17 requested) and removed 39 (8 requested) atoms. Cycle 18: After refmac, R = 0.2318 (Rfree = 0.000) for 3526 atoms. Found 16 (16 requested) and removed 22 (8 requested) atoms. Cycle 19: After refmac, R = 0.2678 (Rfree = 0.000) for 3505 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 20: After refmac, R = 0.2661 (Rfree = 0.000) for 3469 atoms. Found 16 (16 requested) and removed 25 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 4.02 Search for helices and strands: 0 residues in 0 chains, 3557 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3577 seeds are put forward Round 1: 176 peptides, 39 chains. Longest chain 9 peptides. Score 0.237 Round 2: 208 peptides, 38 chains. Longest chain 10 peptides. Score 0.353 Round 3: 194 peptides, 33 chains. Longest chain 11 peptides. Score 0.376 Round 4: 208 peptides, 35 chains. Longest chain 12 peptides. Score 0.391 Round 5: 207 peptides, 35 chains. Longest chain 13 peptides. Score 0.388 Taking the results from Round 4 Chains 35, Residues 173, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 8032 restraints for refining 3639 atoms. 7350 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2880 (Rfree = 0.000) for 3639 atoms. Found 17 (17 requested) and removed 53 (8 requested) atoms. Cycle 22: After refmac, R = 0.2793 (Rfree = 0.000) for 3568 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 23: After refmac, R = 0.2711 (Rfree = 0.000) for 3521 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. Cycle 24: After refmac, R = 0.2673 (Rfree = 0.000) for 3483 atoms. Found 16 (16 requested) and removed 23 (8 requested) atoms. Cycle 25: After refmac, R = 0.2644 (Rfree = 0.000) for 3454 atoms. Found 16 (16 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.61 3.97 Search for helices and strands: 0 residues in 0 chains, 3552 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3569 seeds are put forward Round 1: 161 peptides, 35 chains. Longest chain 8 peptides. Score 0.242 Round 2: 188 peptides, 37 chains. Longest chain 11 peptides. Score 0.304 Round 3: 208 peptides, 37 chains. Longest chain 10 peptides. Score 0.366 Round 4: 200 peptides, 35 chains. Longest chain 11 peptides. Score 0.368 Round 5: 194 peptides, 35 chains. Longest chain 10 peptides. Score 0.349 Taking the results from Round 4 Chains 35, Residues 165, Estimated correctness of the model 0.0 % 3 chains (10 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 7467 restraints for refining 3463 atoms. 6822 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2829 (Rfree = 0.000) for 3463 atoms. Found 16 (16 requested) and removed 49 (8 requested) atoms. Cycle 27: After refmac, R = 0.2697 (Rfree = 0.000) for 3400 atoms. Found 16 (16 requested) and removed 35 (8 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2264 (Rfree = 0.000) for 3368 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 29: After refmac, R = 0.2378 (Rfree = 0.000) for 3354 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 30: After refmac, R = 0.2615 (Rfree = 0.000) for 3344 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 4.08 Search for helices and strands: 0 residues in 0 chains, 3455 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3467 seeds are put forward Round 1: 155 peptides, 33 chains. Longest chain 9 peptides. Score 0.250 Round 2: 183 peptides, 35 chains. Longest chain 10 peptides. Score 0.315 Round 3: 178 peptides, 32 chains. Longest chain 13 peptides. Score 0.340 Round 4: 178 peptides, 34 chains. Longest chain 10 peptides. Score 0.313 Round 5: 177 peptides, 32 chains. Longest chain 10 peptides. Score 0.337 Taking the results from Round 3 Chains 32, Residues 146, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 7395 restraints for refining 3440 atoms. 6811 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2770 (Rfree = 0.000) for 3440 atoms. Found 16 (16 requested) and removed 32 (8 requested) atoms. Cycle 32: After refmac, R = 0.2759 (Rfree = 0.000) for 3392 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. Cycle 33: After refmac, R = 0.2731 (Rfree = 0.000) for 3361 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 34: After refmac, R = 0.2653 (Rfree = 0.000) for 3345 atoms. Found 15 (15 requested) and removed 19 (7 requested) atoms. Cycle 35: After refmac, R = 0.2714 (Rfree = 0.000) for 3331 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.61 3.97 Search for helices and strands: 0 residues in 0 chains, 3439 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3457 seeds are put forward Round 1: 123 peptides, 26 chains. Longest chain 9 peptides. Score 0.241 Round 2: 168 peptides, 33 chains. Longest chain 10 peptides. Score 0.294 Round 3: 178 peptides, 34 chains. Longest chain 8 peptides. Score 0.313 Round 4: 161 peptides, 32 chains. Longest chain 9 peptides. Score 0.285 Round 5: 168 peptides, 31 chains. Longest chain 9 peptides. Score 0.322 Taking the results from Round 5 Chains 31, Residues 137, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 7417 restraints for refining 3436 atoms. 6880 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2825 (Rfree = 0.000) for 3436 atoms. Found 16 (16 requested) and removed 49 (8 requested) atoms. Cycle 37: After refmac, R = 0.2782 (Rfree = 0.000) for 3386 atoms. Found 16 (16 requested) and removed 42 (8 requested) atoms. Cycle 38: After refmac, R = 0.2752 (Rfree = 0.000) for 3347 atoms. Found 15 (15 requested) and removed 30 (7 requested) atoms. Cycle 39: After refmac, R = 0.2221 (Rfree = 0.000) for 3317 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 40: After refmac, R = 0.2645 (Rfree = 0.000) for 3310 atoms. Found 15 (15 requested) and removed 25 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 4.08 Search for helices and strands: 0 residues in 0 chains, 3391 seeds are put forward NCS extension: 0 residues added, 3391 seeds are put forward Round 1: 102 peptides, 24 chains. Longest chain 6 peptides. Score 0.192 Round 2: 131 peptides, 28 chains. Longest chain 9 peptides. Score 0.239 Round 3: 134 peptides, 27 chains. Longest chain 8 peptides. Score 0.265 Round 4: 141 peptides, 27 chains. Longest chain 9 peptides. Score 0.290 Round 5: 138 peptides, 25 chains. Longest chain 10 peptides. Score 0.309 Taking the results from Round 5 Chains 25, Residues 113, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 4616 reflections ( 99.29 % complete ) and 7468 restraints for refining 3389 atoms. 7005 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2966 (Rfree = 0.000) for 3389 atoms. Found 16 (16 requested) and removed 45 (8 requested) atoms. Cycle 42: After refmac, R = 0.2874 (Rfree = 0.000) for 3346 atoms. Found 15 (15 requested) and removed 37 (7 requested) atoms. Cycle 43: After refmac, R = 0.2921 (Rfree = 0.000) for 3314 atoms. Found 15 (15 requested) and removed 31 (7 requested) atoms. Cycle 44: After refmac, R = 0.2942 (Rfree = 0.000) for 3271 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. Cycle 45: After refmac, R = 0.2459 (Rfree = 0.000) for 3260 atoms. Found 15 (15 requested) and removed 15 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 4.08 Search for helices and strands: 0 residues in 0 chains, 3332 seeds are put forward NCS extension: 9 residues added (0 deleted due to clashes), 3341 seeds are put forward Round 1: 130 peptides, 29 chains. Longest chain 7 peptides. Score 0.220 Round 2: 134 peptides, 26 chains. Longest chain 9 peptides. Score 0.280 Round 3: 132 peptides, 28 chains. Longest chain 11 peptides. Score 0.243 Round 4: 118 peptides, 23 chains. Longest chain 8 peptides. Score 0.270 Round 5: 114 peptides, 22 chains. Longest chain 10 peptides. Score 0.271 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 108, 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 2f4p-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4616 reflections ( 99.29 % complete ) and 6584 restraints for refining 3081 atoms. 6178 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2933 (Rfree = 0.000) for 3081 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 47: After refmac, R = 0.2814 (Rfree = 0.000) for 3059 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2285 (Rfree = 0.000) for 3044 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2153 (Rfree = 0.000) for 3032 atoms. TimeTaking 43.37