Mon 24 Dec 00:22:15 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 2fno-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fno-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fno-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-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/2fno-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-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 00:22:19 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/2fno-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fno-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 379 and 0 Target number of residues in the AU: 379 Target solvent content: 0.6507 Checking the provided sequence file Detected sequence length: 248 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 496 Adjusted target solvent content: 0.54 Input MTZ file: 2fno-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: 5 Cell parameters: 110.204 50.261 117.660 90.000 115.716 90.000 Input sequence file: 2fno-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3968 target number of atoms Had to go as low as 0.80 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: 106.006 3.800 Wilson plot Bfac: 78.04 5866 reflections ( 99.07 % complete ) and 0 restraints for refining 4378 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3335 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3462 (Rfree = 0.000) for 4378 atoms. Found 24 (24 requested) and removed 46 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 4471 seeds are put forward NCS extension: 0 residues added, 4471 seeds are put forward Round 1: 202 peptides, 40 chains. Longest chain 9 peptides. Score 0.303 Round 2: 224 peptides, 38 chains. Longest chain 15 peptides. Score 0.392 Round 3: 241 peptides, 39 chains. Longest chain 11 peptides. Score 0.427 Round 4: 259 peptides, 38 chains. Longest chain 15 peptides. Score 0.484 Round 5: 270 peptides, 41 chains. Longest chain 14 peptides. Score 0.479 Taking the results from Round 4 Chains 38, Residues 221, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8276 restraints for refining 3587 atoms. 7414 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2449 (Rfree = 0.000) for 3587 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 2: After refmac, R = 0.2332 (Rfree = 0.000) for 3543 atoms. Found 18 (19 requested) and removed 26 (9 requested) atoms. Cycle 3: After refmac, R = 0.2181 (Rfree = 0.000) for 3513 atoms. Found 15 (19 requested) and removed 21 (9 requested) atoms. Cycle 4: After refmac, R = 0.1844 (Rfree = 0.000) for 3488 atoms. Found 7 (19 requested) and removed 13 (9 requested) atoms. Cycle 5: After refmac, R = 0.1761 (Rfree = 0.000) for 3471 atoms. Found 4 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 3624 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 3636 seeds are put forward Round 1: 216 peptides, 38 chains. Longest chain 12 peptides. Score 0.369 Round 2: 236 peptides, 32 chains. Longest chain 14 peptides. Score 0.494 Round 3: 253 peptides, 37 chains. Longest chain 15 peptides. Score 0.480 Round 4: 249 peptides, 35 chains. Longest chain 14 peptides. Score 0.492 Round 5: 237 peptides, 35 chains. Longest chain 17 peptides. Score 0.462 Taking the results from Round 2 Chains 33, Residues 204, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8192 restraints for refining 3573 atoms. 7387 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2319 (Rfree = 0.000) for 3573 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 7: After refmac, R = 0.2187 (Rfree = 0.000) for 3540 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Cycle 8: After refmac, R = 0.2112 (Rfree = 0.000) for 3517 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 9: After refmac, R = 0.2041 (Rfree = 0.000) for 3511 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 10: After refmac, R = 0.1940 (Rfree = 0.000) for 3500 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.41 Search for helices and strands: 0 residues in 0 chains, 3671 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3682 seeds are put forward Round 1: 188 peptides, 34 chains. Longest chain 9 peptides. Score 0.338 Round 2: 213 peptides, 31 chains. Longest chain 13 peptides. Score 0.446 Round 3: 238 peptides, 37 chains. Longest chain 14 peptides. Score 0.442 Round 4: 241 peptides, 36 chains. Longest chain 18 peptides. Score 0.461 Round 5: 240 peptides, 33 chains. Longest chain 17 peptides. Score 0.492 Taking the results from Round 5 Chains 36, Residues 207, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8135 restraints for refining 3588 atoms. 7287 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2278 (Rfree = 0.000) for 3588 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Cycle 12: After refmac, R = 0.1998 (Rfree = 0.000) for 3557 atoms. Found 15 (19 requested) and removed 16 (9 requested) atoms. Cycle 13: After refmac, R = 0.1994 (Rfree = 0.000) for 3544 atoms. Found 12 (19 requested) and removed 21 (9 requested) atoms. Cycle 14: After refmac, R = 0.1837 (Rfree = 0.000) for 3530 atoms. Found 14 (19 requested) and removed 17 (9 requested) atoms. Cycle 15: After refmac, R = 0.1882 (Rfree = 0.000) for 3522 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 3667 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3681 seeds are put forward Round 1: 230 peptides, 44 chains. Longest chain 8 peptides. Score 0.336 Round 2: 255 peptides, 41 chains. Longest chain 11 peptides. Score 0.440 Round 3: 234 peptides, 38 chains. Longest chain 12 peptides. Score 0.419 Round 4: 247 peptides, 38 chains. Longest chain 13 peptides. Score 0.454 Round 5: 231 peptides, 35 chains. Longest chain 13 peptides. Score 0.447 Taking the results from Round 4 Chains 38, Residues 209, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8492 restraints for refining 3588 atoms. 7694 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2269 (Rfree = 0.000) for 3588 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 17: After refmac, R = 0.2038 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 18: After refmac, R = 0.2048 (Rfree = 0.000) for 3547 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 19: After refmac, R = 0.1968 (Rfree = 0.000) for 3541 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 20: After refmac, R = 0.1968 (Rfree = 0.000) for 3533 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.64 3.45 Search for helices and strands: 0 residues in 0 chains, 3746 seeds are put forward NCS extension: 0 residues added, 3746 seeds are put forward Round 1: 194 peptides, 38 chains. Longest chain 9 peptides. Score 0.304 Round 2: 210 peptides, 37 chains. Longest chain 10 peptides. Score 0.365 Round 3: 207 peptides, 33 chains. Longest chain 16 peptides. Score 0.406 Round 4: 218 peptides, 34 chains. Longest chain 11 peptides. Score 0.424 Round 5: 208 peptides, 30 chains. Longest chain 16 peptides. Score 0.445 Taking the results from Round 5 Chains 30, Residues 178, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8543 restraints for refining 3589 atoms. 7841 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2274 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 22: After refmac, R = 0.2192 (Rfree = 0.000) for 3562 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 23: After refmac, R = 0.2071 (Rfree = 0.000) for 3556 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 24: After refmac, R = 0.2111 (Rfree = 0.000) for 3554 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 25: After refmac, R = 0.1983 (Rfree = 0.000) for 3553 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.46 Search for helices and strands: 0 residues in 0 chains, 3704 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 3722 seeds are put forward Round 1: 186 peptides, 37 chains. Longest chain 10 peptides. Score 0.293 Round 2: 208 peptides, 34 chains. Longest chain 15 peptides. Score 0.396 Round 3: 204 peptides, 29 chains. Longest chain 18 peptides. Score 0.446 Round 4: 202 peptides, 29 chains. Longest chain 22 peptides. Score 0.441 Round 5: 211 peptides, 34 chains. Longest chain 12 peptides. Score 0.405 Taking the results from Round 3 Chains 29, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8633 restraints for refining 3588 atoms. 7962 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2218 (Rfree = 0.000) for 3588 atoms. Found 19 (19 requested) and removed 16 (9 requested) atoms. Cycle 27: After refmac, R = 0.2114 (Rfree = 0.000) for 3572 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 28: After refmac, R = 0.2268 (Rfree = 0.000) for 3570 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 29: After refmac, R = 0.2021 (Rfree = 0.000) for 3560 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 30: After refmac, R = 0.1946 (Rfree = 0.000) for 3561 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 3692 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 3720 seeds are put forward Round 1: 177 peptides, 37 chains. Longest chain 12 peptides. Score 0.265 Round 2: 196 peptides, 37 chains. Longest chain 11 peptides. Score 0.323 Round 3: 198 peptides, 33 chains. Longest chain 18 peptides. Score 0.380 Round 4: 197 peptides, 38 chains. Longest chain 10 peptides. Score 0.314 Round 5: 211 peptides, 38 chains. Longest chain 16 peptides. Score 0.355 Taking the results from Round 3 Chains 33, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8564 restraints for refining 3589 atoms. 7937 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2074 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 32: After refmac, R = 0.2027 (Rfree = 0.000) for 3580 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 33: After refmac, R = 0.1990 (Rfree = 0.000) for 3576 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 34: After refmac, R = 0.1891 (Rfree = 0.000) for 3569 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 35: After refmac, R = 0.1947 (Rfree = 0.000) for 3571 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 3743 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3766 seeds are put forward Round 1: 172 peptides, 38 chains. Longest chain 8 peptides. Score 0.235 Round 2: 187 peptides, 34 chains. Longest chain 9 peptides. Score 0.335 Round 3: 190 peptides, 33 chains. Longest chain 12 peptides. Score 0.357 Round 4: 189 peptides, 31 chains. Longest chain 10 peptides. Score 0.380 Round 5: 195 peptides, 31 chains. Longest chain 15 peptides. Score 0.397 Taking the results from Round 5 Chains 31, Residues 164, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8648 restraints for refining 3589 atoms. 7994 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2159 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 37: After refmac, R = 0.2153 (Rfree = 0.000) for 3575 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 38: After refmac, R = 0.1911 (Rfree = 0.000) for 3562 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 39: After refmac, R = 0.2138 (Rfree = 0.000) for 3559 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 40: After refmac, R = 0.1840 (Rfree = 0.000) for 3550 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.65 3.46 Search for helices and strands: 0 residues in 0 chains, 3681 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3705 seeds are put forward Round 1: 154 peptides, 32 chains. Longest chain 7 peptides. Score 0.258 Round 2: 185 peptides, 34 chains. Longest chain 11 peptides. Score 0.329 Round 3: 185 peptides, 33 chains. Longest chain 9 peptides. Score 0.342 Round 4: 190 peptides, 35 chains. Longest chain 11 peptides. Score 0.331 Round 5: 186 peptides, 35 chains. Longest chain 10 peptides. Score 0.319 Taking the results from Round 3 Chains 33, Residues 152, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5866 reflections ( 99.07 % complete ) and 8689 restraints for refining 3589 atoms. 8114 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2048 (Rfree = 0.000) for 3589 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 42: After refmac, R = 0.2055 (Rfree = 0.000) for 3581 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 43: After refmac, R = 0.1966 (Rfree = 0.000) for 3559 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 44: After refmac, R = 0.1888 (Rfree = 0.000) for 3551 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 45: After refmac, R = 0.1847 (Rfree = 0.000) for 3554 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 3.45 Search for helices and strands: 0 residues in 0 chains, 3691 seeds are put forward NCS extension: 0 residues added, 3691 seeds are put forward Round 1: 146 peptides, 32 chains. Longest chain 7 peptides. Score 0.231 Round 2: 174 peptides, 32 chains. Longest chain 9 peptides. Score 0.322 Round 3: 178 peptides, 31 chains. Longest chain 9 peptides. Score 0.347 Round 4: 165 peptides, 29 chains. Longest chain 8 peptides. Score 0.335 Round 5: 178 peptides, 31 chains. Longest chain 9 peptides. Score 0.347 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 31, Residues 147, 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 2fno-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5866 reflections ( 99.07 % complete ) and 8695 restraints for refining 3589 atoms. 8138 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1970 (Rfree = 0.000) for 3589 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1940 (Rfree = 0.000) for 3562 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1946 (Rfree = 0.000) for 3543 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1916 (Rfree = 0.000) for 3527 atoms. TimeTaking 42.97