Mon 24 Dec 00:17:17 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-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2f4p-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2f4p-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.8-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-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.8-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 00:17:22 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-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4p-3.8-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 373 and 0 Target number of residues in the AU: 373 Target solvent content: 0.6398 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-3.8-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-3.8-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 3.800 Wilson plot Bfac: 71.67 5384 reflections ( 99.39 % complete ) and 0 restraints for refining 5211 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3396 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3328 (Rfree = 0.000) for 5211 atoms. Found 28 (28 requested) and removed 74 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 5242 seeds are put forward NCS extension: 0 residues added, 5242 seeds are put forward Round 1: 180 peptides, 40 chains. Longest chain 7 peptides. Score 0.236 Round 2: 233 peptides, 40 chains. Longest chain 9 peptides. Score 0.401 Round 3: 266 peptides, 41 chains. Longest chain 19 peptides. Score 0.479 Round 4: 278 peptides, 46 chains. Longest chain 11 peptides. Score 0.454 Round 5: 279 peptides, 44 chains. Longest chain 15 peptides. Score 0.479 Taking the results from Round 5 Chains 44, Residues 235, Estimated correctness of the model 0.0 % 4 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 10044 restraints for refining 4253 atoms. 9106 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2936 (Rfree = 0.000) for 4253 atoms. Found 23 (23 requested) and removed 92 (11 requested) atoms. Cycle 2: After refmac, R = 0.2952 (Rfree = 0.000) for 4112 atoms. Found 21 (23 requested) and removed 56 (11 requested) atoms. Cycle 3: After refmac, R = 0.2889 (Rfree = 0.000) for 3996 atoms. Found 22 (22 requested) and removed 44 (11 requested) atoms. Cycle 4: After refmac, R = 0.3110 (Rfree = 0.000) for 3928 atoms. Found 21 (21 requested) and removed 56 (10 requested) atoms. Cycle 5: After refmac, R = 0.2934 (Rfree = 0.000) for 3831 atoms. Found 21 (21 requested) and removed 42 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.92 Search for helices and strands: 0 residues in 0 chains, 3931 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3948 seeds are put forward Round 1: 225 peptides, 42 chains. Longest chain 16 peptides. Score 0.353 Round 2: 257 peptides, 43 chains. Longest chain 13 peptides. Score 0.432 Round 3: 290 peptides, 44 chains. Longest chain 21 peptides. Score 0.507 Round 4: 292 peptides, 41 chains. Longest chain 15 peptides. Score 0.543 Round 5: 301 peptides, 42 chains. Longest chain 19 peptides. Score 0.554 Taking the results from Round 5 Chains 42, Residues 259, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8536 restraints for refining 3869 atoms. 7542 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2870 (Rfree = 0.000) for 3869 atoms. Found 21 (21 requested) and removed 62 (10 requested) atoms. Cycle 7: After refmac, R = 0.2625 (Rfree = 0.000) for 3791 atoms. Found 20 (21 requested) and removed 43 (10 requested) atoms. Cycle 8: After refmac, R = 0.2744 (Rfree = 0.000) for 3723 atoms. Found 20 (20 requested) and removed 66 (10 requested) atoms. Cycle 9: After refmac, R = 0.2508 (Rfree = 0.000) for 3634 atoms. Found 20 (20 requested) and removed 20 (10 requested) atoms. Cycle 10: After refmac, R = 0.2644 (Rfree = 0.000) for 3613 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.54 3.89 Search for helices and strands: 0 residues in 0 chains, 3748 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3769 seeds are put forward Round 1: 230 peptides, 45 chains. Longest chain 14 peptides. Score 0.329 Round 2: 262 peptides, 45 chains. Longest chain 15 peptides. Score 0.422 Round 3: 270 peptides, 42 chains. Longest chain 14 peptides. Score 0.478 Round 4: 274 peptides, 43 chains. Longest chain 18 peptides. Score 0.477 Round 5: 281 peptides, 44 chains. Longest chain 14 peptides. Score 0.484 Taking the results from Round 5 Chains 44, Residues 237, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8415 restraints for refining 3810 atoms. 7489 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2532 (Rfree = 0.000) for 3810 atoms. Found 20 (20 requested) and removed 51 (10 requested) atoms. Cycle 12: After refmac, R = 0.2754 (Rfree = 0.000) for 3730 atoms. Found 20 (20 requested) and removed 54 (10 requested) atoms. Cycle 13: After refmac, R = 0.2662 (Rfree = 0.000) for 3649 atoms. Found 20 (20 requested) and removed 46 (10 requested) atoms. Cycle 14: After refmac, R = 0.2574 (Rfree = 0.000) for 3594 atoms. Found 19 (19 requested) and removed 43 (9 requested) atoms. Cycle 15: After refmac, R = 0.2259 (Rfree = 0.000) for 3547 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.50 3.84 Search for helices and strands: 0 residues in 0 chains, 3644 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3659 seeds are put forward Round 1: 203 peptides, 43 chains. Longest chain 8 peptides. Score 0.271 Round 2: 244 peptides, 43 chains. Longest chain 11 peptides. Score 0.396 Round 3: 252 peptides, 42 chains. Longest chain 12 peptides. Score 0.430 Round 4: 251 peptides, 42 chains. Longest chain 18 peptides. Score 0.427 Round 5: 254 peptides, 40 chains. Longest chain 12 peptides. Score 0.459 Taking the results from Round 5 Chains 40, Residues 214, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8269 restraints for refining 3738 atoms. 7442 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2737 (Rfree = 0.000) for 3738 atoms. Found 20 (20 requested) and removed 68 (10 requested) atoms. Cycle 17: After refmac, R = 0.2547 (Rfree = 0.000) for 3663 atoms. Found 20 (20 requested) and removed 33 (10 requested) atoms. Cycle 18: After refmac, R = 0.2635 (Rfree = 0.000) for 3606 atoms. Found 20 (20 requested) and removed 33 (10 requested) atoms. Cycle 19: After refmac, R = 0.2404 (Rfree = 0.000) for 3570 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 20: After refmac, R = 0.2347 (Rfree = 0.000) for 3557 atoms. Found 17 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.53 3.88 Search for helices and strands: 0 residues in 0 chains, 3668 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3684 seeds are put forward Round 1: 210 peptides, 43 chains. Longest chain 11 peptides. Score 0.293 Round 2: 252 peptides, 45 chains. Longest chain 15 peptides. Score 0.394 Round 3: 273 peptides, 47 chains. Longest chain 13 peptides. Score 0.429 Round 4: 271 peptides, 42 chains. Longest chain 15 peptides. Score 0.481 Round 5: 259 peptides, 38 chains. Longest chain 16 peptides. Score 0.495 Taking the results from Round 5 Chains 38, Residues 221, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8259 restraints for refining 3758 atoms. 7369 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2688 (Rfree = 0.000) for 3758 atoms. Found 20 (20 requested) and removed 52 (10 requested) atoms. Cycle 22: After refmac, R = 0.2720 (Rfree = 0.000) for 3689 atoms. Found 20 (20 requested) and removed 48 (10 requested) atoms. Cycle 23: After refmac, R = 0.2418 (Rfree = 0.000) for 3637 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 24: After refmac, R = 0.2369 (Rfree = 0.000) for 3611 atoms. Found 19 (19 requested) and removed 40 (9 requested) atoms. Cycle 25: After refmac, R = 0.2241 (Rfree = 0.000) for 3573 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.55 3.90 Search for helices and strands: 0 residues in 0 chains, 3686 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3710 seeds are put forward Round 1: 193 peptides, 41 chains. Longest chain 7 peptides. Score 0.266 Round 2: 230 peptides, 41 chains. Longest chain 10 peptides. Score 0.380 Round 3: 251 peptides, 42 chains. Longest chain 12 peptides. Score 0.427 Round 4: 242 peptides, 39 chains. Longest chain 17 peptides. Score 0.438 Round 5: 241 peptides, 38 chains. Longest chain 18 peptides. Score 0.448 Taking the results from Round 5 Chains 40, Residues 203, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 8264 restraints for refining 3730 atoms. 7443 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2942 (Rfree = 0.000) for 3730 atoms. Found 20 (20 requested) and removed 89 (10 requested) atoms. Cycle 27: After refmac, R = 0.2564 (Rfree = 0.000) for 3627 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 28: After refmac, R = 0.2563 (Rfree = 0.000) for 3592 atoms. Found 19 (19 requested) and removed 33 (9 requested) atoms. Cycle 29: After refmac, R = 0.2178 (Rfree = 0.000) for 3568 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 30: After refmac, R = 0.1898 (Rfree = 0.000) for 3556 atoms. Found 11 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.50 3.84 Search for helices and strands: 0 residues in 0 chains, 3656 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3670 seeds are put forward Round 1: 183 peptides, 38 chains. Longest chain 9 peptides. Score 0.274 Round 2: 232 peptides, 40 chains. Longest chain 13 peptides. Score 0.398 Round 3: 233 peptides, 41 chains. Longest chain 12 peptides. Score 0.389 Round 4: 236 peptides, 37 chains. Longest chain 14 peptides. Score 0.446 Round 5: 247 peptides, 38 chains. Longest chain 13 peptides. Score 0.464 Taking the results from Round 5 Chains 38, Residues 209, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 7986 restraints for refining 3679 atoms. 7160 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2479 (Rfree = 0.000) for 3679 atoms. Found 20 (20 requested) and removed 38 (10 requested) atoms. Cycle 32: After refmac, R = 0.2340 (Rfree = 0.000) for 3634 atoms. Found 20 (20 requested) and removed 38 (10 requested) atoms. Cycle 33: After refmac, R = 0.2296 (Rfree = 0.000) for 3595 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 34: After refmac, R = 0.2267 (Rfree = 0.000) for 3576 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 35: After refmac, R = 0.2185 (Rfree = 0.000) for 3567 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.82 Search for helices and strands: 0 residues in 0 chains, 3715 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3733 seeds are put forward Round 1: 168 peptides, 38 chains. Longest chain 9 peptides. Score 0.223 Round 2: 203 peptides, 42 chains. Longest chain 10 peptides. Score 0.284 Round 3: 220 peptides, 41 chains. Longest chain 10 peptides. Score 0.350 Round 4: 230 peptides, 42 chains. Longest chain 12 peptides. Score 0.367 Round 5: 232 peptides, 43 chains. Longest chain 10 peptides. Score 0.361 Taking the results from Round 4 Chains 42, Residues 188, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 7755 restraints for refining 3531 atoms. 7045 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2475 (Rfree = 0.000) for 3531 atoms. Found 19 (19 requested) and removed 33 (9 requested) atoms. Cycle 37: After refmac, R = 0.2416 (Rfree = 0.000) for 3492 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 38: After refmac, R = 0.2294 (Rfree = 0.000) for 3479 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 39: After refmac, R = 0.2276 (Rfree = 0.000) for 3466 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 40: After refmac, R = 0.2274 (Rfree = 0.000) for 3441 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.87 Search for helices and strands: 0 residues in 0 chains, 3615 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3632 seeds are put forward Round 1: 167 peptides, 38 chains. Longest chain 7 peptides. Score 0.220 Round 2: 184 peptides, 35 chains. Longest chain 12 peptides. Score 0.318 Round 3: 188 peptides, 35 chains. Longest chain 10 peptides. Score 0.331 Round 4: 180 peptides, 33 chains. Longest chain 13 peptides. Score 0.333 Round 5: 189 peptides, 33 chains. Longest chain 10 peptides. Score 0.361 Taking the results from Round 5 Chains 33, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5384 reflections ( 99.39 % complete ) and 7789 restraints for refining 3544 atoms. 7198 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2397 (Rfree = 0.000) for 3544 atoms. Found 19 (19 requested) and removed 50 (9 requested) atoms. Cycle 42: After refmac, R = 0.2725 (Rfree = 0.000) for 3502 atoms. Found 19 (19 requested) and removed 52 (9 requested) atoms. Cycle 43: After refmac, R = 0.2310 (Rfree = 0.000) for 3451 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 44: After refmac, R = 0.2464 (Rfree = 0.000) for 3435 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. Cycle 45: After refmac, R = 0.2459 (Rfree = 0.000) for 3417 atoms. Found 18 (18 requested) and removed 30 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.88 Search for helices and strands: 0 residues in 0 chains, 3519 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 3530 seeds are put forward Round 1: 129 peptides, 29 chains. Longest chain 11 peptides. Score 0.217 Round 2: 176 peptides, 36 chains. Longest chain 10 peptides. Score 0.278 Round 3: 164 peptides, 30 chains. Longest chain 9 peptides. Score 0.323 Round 4: 179 peptides, 33 chains. Longest chain 9 peptides. Score 0.329 Round 5: 172 peptides, 32 chains. Longest chain 9 peptides. Score 0.321 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 146, 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-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5384 reflections ( 99.39 % complete ) and 7689 restraints for refining 3498 atoms. 7138 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2384 (Rfree = 0.000) for 3498 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2629 (Rfree = 0.000) for 3476 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2160 (Rfree = 0.000) for 3454 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2408 (Rfree = 0.000) for 3439 atoms. TimeTaking 51.32