Sun 23 Dec 22:22:55 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 2p7i-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p7i-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p7i-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.8-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/2p7i-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.8-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 22:23:04 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/2p7i-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.8-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 337 and 0 Target number of residues in the AU: 337 Target solvent content: 0.6663 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 500 Adjusted target solvent content: 0.50 Input MTZ file: 2p7i-3.8-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: 97 Cell parameters: 120.769 120.769 149.904 90.000 90.000 90.000 Input sequence file: 2p7i-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4000 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: 94.045 3.800 Wilson plot Bfac: 89.21 5722 reflections ( 99.65 % complete ) and 0 restraints for refining 4422 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3381 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3281 (Rfree = 0.000) for 4422 atoms. Found 11 (24 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.67 3.67 Search for helices and strands: 0 residues in 0 chains, 4494 seeds are put forward NCS extension: 0 residues added, 4494 seeds are put forward Round 1: 183 peptides, 39 chains. Longest chain 8 peptides. Score 0.262 Round 2: 237 peptides, 40 chains. Longest chain 13 peptides. Score 0.417 Round 3: 257 peptides, 39 chains. Longest chain 13 peptides. Score 0.484 Round 4: 266 peptides, 42 chains. Longest chain 15 peptides. Score 0.473 Round 5: 287 peptides, 36 chains. Longest chain 33 peptides. Score 0.590 Taking the results from Round 5 Chains 40, Residues 251, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 7897 restraints for refining 3617 atoms. 6838 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2969 (Rfree = 0.000) for 3617 atoms. Found 18 (19 requested) and removed 23 (9 requested) atoms. Cycle 2: After refmac, R = 0.2557 (Rfree = 0.000) for 3526 atoms. Found 10 (19 requested) and removed 23 (9 requested) atoms. Cycle 3: After refmac, R = 0.2469 (Rfree = 0.000) for 3470 atoms. Found 8 (19 requested) and removed 18 (9 requested) atoms. Cycle 4: After refmac, R = 0.2341 (Rfree = 0.000) for 3436 atoms. Found 9 (19 requested) and removed 13 (9 requested) atoms. Cycle 5: After refmac, R = 0.2372 (Rfree = 0.000) for 3414 atoms. Found 10 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.67 Search for helices and strands: 0 residues in 0 chains, 3558 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3571 seeds are put forward Round 1: 250 peptides, 48 chains. Longest chain 10 peptides. Score 0.355 Round 2: 263 peptides, 38 chains. Longest chain 20 peptides. Score 0.511 Round 3: 271 peptides, 38 chains. Longest chain 20 peptides. Score 0.531 Round 4: 274 peptides, 36 chains. Longest chain 24 peptides. Score 0.560 Round 5: 272 peptides, 38 chains. Longest chain 15 peptides. Score 0.534 Taking the results from Round 4 Chains 36, Residues 238, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8253 restraints for refining 3616 atoms. 7337 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2383 (Rfree = 0.000) for 3616 atoms. Found 4 (19 requested) and removed 20 (9 requested) atoms. Cycle 7: After refmac, R = 0.2351 (Rfree = 0.000) for 3556 atoms. Found 8 (19 requested) and removed 11 (9 requested) atoms. Cycle 8: After refmac, R = 0.2422 (Rfree = 0.000) for 3536 atoms. Found 9 (19 requested) and removed 15 (9 requested) atoms. Cycle 9: After refmac, R = 0.2388 (Rfree = 0.000) for 3510 atoms. Found 4 (19 requested) and removed 17 (9 requested) atoms. Cycle 10: After refmac, R = 0.2469 (Rfree = 0.000) for 3483 atoms. Found 8 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.65 Search for helices and strands: 0 residues in 0 chains, 3649 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 3661 seeds are put forward Round 1: 219 peptides, 39 chains. Longest chain 12 peptides. Score 0.377 Round 2: 262 peptides, 38 chains. Longest chain 23 peptides. Score 0.509 Round 3: 278 peptides, 45 chains. Longest chain 16 peptides. Score 0.471 Round 4: 263 peptides, 35 chains. Longest chain 16 peptides. Score 0.544 Round 5: 245 peptides, 34 chains. Longest chain 20 peptides. Score 0.511 Taking the results from Round 4 Chains 35, Residues 228, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8123 restraints for refining 3618 atoms. 7162 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2415 (Rfree = 0.000) for 3618 atoms. Found 6 (19 requested) and removed 16 (9 requested) atoms. Cycle 12: After refmac, R = 0.2410 (Rfree = 0.000) for 3562 atoms. Found 13 (19 requested) and removed 13 (9 requested) atoms. Cycle 13: After refmac, R = 0.2062 (Rfree = 0.000) for 3537 atoms. Found 7 (19 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2516 (Rfree = 0.000) for 3519 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Cycle 15: After refmac, R = 0.2299 (Rfree = 0.000) for 3494 atoms. Found 11 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 3626 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 3647 seeds are put forward Round 1: 209 peptides, 41 chains. Longest chain 10 peptides. Score 0.319 Round 2: 259 peptides, 43 chains. Longest chain 17 peptides. Score 0.442 Round 3: 257 peptides, 39 chains. Longest chain 14 peptides. Score 0.484 Round 4: 275 peptides, 45 chains. Longest chain 17 peptides. Score 0.463 Round 5: 263 peptides, 38 chains. Longest chain 16 peptides. Score 0.511 Taking the results from Round 5 Chains 38, Residues 225, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8339 restraints for refining 3618 atoms. 7437 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2436 (Rfree = 0.000) for 3618 atoms. Found 16 (19 requested) and removed 22 (9 requested) atoms. Cycle 17: After refmac, R = 0.2245 (Rfree = 0.000) for 3573 atoms. Found 10 (19 requested) and removed 16 (9 requested) atoms. Cycle 18: After refmac, R = 0.2269 (Rfree = 0.000) for 3554 atoms. Found 12 (19 requested) and removed 16 (9 requested) atoms. Cycle 19: After refmac, R = 0.1894 (Rfree = 0.000) for 3536 atoms. Found 5 (19 requested) and removed 14 (9 requested) atoms. Cycle 20: After refmac, R = 0.1821 (Rfree = 0.000) for 3519 atoms. Found 5 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.71 Search for helices and strands: 0 residues in 0 chains, 3616 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 3642 seeds are put forward Round 1: 206 peptides, 39 chains. Longest chain 9 peptides. Score 0.337 Round 2: 244 peptides, 39 chains. Longest chain 16 peptides. Score 0.449 Round 3: 249 peptides, 38 chains. Longest chain 16 peptides. Score 0.474 Round 4: 249 peptides, 36 chains. Longest chain 16 peptides. Score 0.498 Round 5: 258 peptides, 38 chains. Longest chain 16 peptides. Score 0.498 Taking the results from Round 5 Chains 39, Residues 220, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8400 restraints for refining 3617 atoms. 7519 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2316 (Rfree = 0.000) for 3617 atoms. Found 13 (19 requested) and removed 21 (9 requested) atoms. Cycle 22: After refmac, R = 0.2272 (Rfree = 0.000) for 3588 atoms. Found 11 (19 requested) and removed 16 (9 requested) atoms. Cycle 23: After refmac, R = 0.2193 (Rfree = 0.000) for 3569 atoms. Found 10 (19 requested) and removed 18 (9 requested) atoms. Cycle 24: After refmac, R = 0.2295 (Rfree = 0.000) for 3554 atoms. Found 10 (19 requested) and removed 18 (9 requested) atoms. Cycle 25: After refmac, R = 0.1756 (Rfree = 0.000) for 3531 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.68 3.68 Search for helices and strands: 0 residues in 0 chains, 3673 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3693 seeds are put forward Round 1: 183 peptides, 39 chains. Longest chain 10 peptides. Score 0.262 Round 2: 229 peptides, 37 chains. Longest chain 15 peptides. Score 0.431 Round 3: 244 peptides, 40 chains. Longest chain 13 peptides. Score 0.437 Round 4: 241 peptides, 37 chains. Longest chain 17 peptides. Score 0.465 Round 5: 249 peptides, 36 chains. Longest chain 18 peptides. Score 0.498 Taking the results from Round 5 Chains 37, Residues 213, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8300 restraints for refining 3617 atoms. 7411 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2315 (Rfree = 0.000) for 3617 atoms. Found 7 (19 requested) and removed 14 (9 requested) atoms. Cycle 27: After refmac, R = 0.2134 (Rfree = 0.000) for 3588 atoms. Found 10 (19 requested) and removed 14 (9 requested) atoms. Cycle 28: After refmac, R = 0.2166 (Rfree = 0.000) for 3565 atoms. Found 14 (19 requested) and removed 12 (9 requested) atoms. Cycle 29: After refmac, R = 0.1827 (Rfree = 0.000) for 3546 atoms. Found 3 (19 requested) and removed 12 (9 requested) atoms. Cycle 30: After refmac, R = 0.2130 (Rfree = 0.000) for 3528 atoms. Found 14 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.64 Search for helices and strands: 0 residues in 0 chains, 3614 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3642 seeds are put forward Round 1: 167 peptides, 38 chains. Longest chain 7 peptides. Score 0.221 Round 2: 214 peptides, 45 chains. Longest chain 9 peptides. Score 0.282 Round 3: 222 peptides, 42 chains. Longest chain 10 peptides. Score 0.347 Round 4: 198 peptides, 34 chains. Longest chain 11 peptides. Score 0.378 Round 5: 221 peptides, 37 chains. Longest chain 18 peptides. Score 0.408 Taking the results from Round 5 Chains 37, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8500 restraints for refining 3618 atoms. 7801 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2334 (Rfree = 0.000) for 3618 atoms. Found 16 (19 requested) and removed 17 (9 requested) atoms. Cycle 32: After refmac, R = 0.2293 (Rfree = 0.000) for 3596 atoms. Found 11 (19 requested) and removed 16 (9 requested) atoms. Cycle 33: After refmac, R = 0.2384 (Rfree = 0.000) for 3575 atoms. Found 9 (19 requested) and removed 11 (9 requested) atoms. Cycle 34: After refmac, R = 0.2304 (Rfree = 0.000) for 3551 atoms. Found 8 (19 requested) and removed 12 (9 requested) atoms. Cycle 35: After refmac, R = 0.2331 (Rfree = 0.000) for 3529 atoms. Found 10 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.64 3.64 Search for helices and strands: 0 residues in 0 chains, 3627 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 3651 seeds are put forward Round 1: 145 peptides, 33 chains. Longest chain 10 peptides. Score 0.216 Round 2: 196 peptides, 40 chains. Longest chain 15 peptides. Score 0.291 Round 3: 184 peptides, 38 chains. Longest chain 9 peptides. Score 0.279 Round 4: 181 peptides, 34 chains. Longest chain 15 peptides. Score 0.325 Round 5: 177 peptides, 32 chains. Longest chain 13 peptides. Score 0.340 Taking the results from Round 5 Chains 32, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8689 restraints for refining 3599 atoms. 8141 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2539 (Rfree = 0.000) for 3599 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 37: After refmac, R = 0.2473 (Rfree = 0.000) for 3572 atoms. Found 9 (19 requested) and removed 17 (9 requested) atoms. Cycle 38: After refmac, R = 0.2465 (Rfree = 0.000) for 3552 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 39: After refmac, R = 0.2519 (Rfree = 0.000) for 3550 atoms. Found 11 (19 requested) and removed 16 (9 requested) atoms. Cycle 40: After refmac, R = 0.2649 (Rfree = 0.000) for 3538 atoms. Found 16 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.63 Search for helices and strands: 0 residues in 0 chains, 3642 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3659 seeds are put forward Round 1: 163 peptides, 37 chains. Longest chain 7 peptides. Score 0.221 Round 2: 190 peptides, 36 chains. Longest chain 12 peptides. Score 0.326 Round 3: 178 peptides, 34 chains. Longest chain 8 peptides. Score 0.315 Round 4: 200 peptides, 38 chains. Longest chain 9 peptides. Score 0.331 Round 5: 201 peptides, 35 chains. Longest chain 9 peptides. Score 0.374 Taking the results from Round 5 Chains 35, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5722 reflections ( 99.65 % complete ) and 8083 restraints for refining 3508 atoms. 7454 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2452 (Rfree = 0.000) for 3508 atoms. Found 19 (19 requested) and removed 30 (9 requested) atoms. Cycle 42: After refmac, R = 0.2300 (Rfree = 0.000) for 3476 atoms. Found 12 (19 requested) and removed 13 (9 requested) atoms. Cycle 43: After refmac, R = 0.2241 (Rfree = 0.000) for 3466 atoms. Found 19 (19 requested) and removed 14 (9 requested) atoms. Cycle 44: After refmac, R = 0.2173 (Rfree = 0.000) for 3465 atoms. Found 18 (19 requested) and removed 13 (9 requested) atoms. Cycle 45: After refmac, R = 0.2225 (Rfree = 0.000) for 3461 atoms. Found 18 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.69 Search for helices and strands: 0 residues in 0 chains, 3562 seeds are put forward NCS extension: 0 residues added, 3562 seeds are put forward Round 1: 142 peptides, 31 chains. Longest chain 7 peptides. Score 0.235 Round 2: 169 peptides, 32 chains. Longest chain 11 peptides. Score 0.314 Round 3: 174 peptides, 35 chains. Longest chain 9 peptides. Score 0.288 Round 4: 175 peptides, 32 chains. Longest chain 9 peptides. Score 0.333 Round 5: 196 peptides, 35 chains. Longest chain 11 peptides. Score 0.359 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 161, 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 2p7i-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5722 reflections ( 99.65 % complete ) and 8318 restraints for refining 3561 atoms. 7709 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2544 (Rfree = 0.000) for 3561 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2343 (Rfree = 0.000) for 3535 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2458 (Rfree = 0.000) for 3513 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2589 (Rfree = 0.000) for 3496 atoms. TimeTaking 62.78