Mon 24 Dec 01:11:53 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 2p7i-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p7i-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p7i-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.4-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/2p7i-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.4-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 01:11:58 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/2p7i-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.4-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 355 and 0 Target number of residues in the AU: 355 Target solvent content: 0.6485 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-3.4-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: 97 Cell parameters: 120.769 120.769 149.904 90.000 90.000 90.000 Input sequence file: 2p7i-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4000 target number of atoms Had to go as low as 0.60 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 3.400 Wilson plot Bfac: 76.83 7942 reflections ( 99.75 % complete ) and 0 restraints for refining 4410 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3188 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3084 (Rfree = 0.000) for 4410 atoms. Found 33 (33 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.46 Search for helices and strands: 0 residues in 0 chains, 4508 seeds are put forward NCS extension: 0 residues added, 4508 seeds are put forward Round 1: 246 peptides, 44 chains. Longest chain 13 peptides. Score 0.393 Round 2: 301 peptides, 41 chains. Longest chain 19 peptides. Score 0.571 Round 3: 314 peptides, 34 chains. Longest chain 22 peptides. Score 0.664 Round 4: 324 peptides, 32 chains. Longest chain 22 peptides. Score 0.699 Round 5: 317 peptides, 33 chains. Longest chain 19 peptides. Score 0.679 Taking the results from Round 4 Chains 33, Residues 292, Estimated correctness of the model 57.6 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8095 restraints for refining 3636 atoms. 6932 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2599 (Rfree = 0.000) for 3636 atoms. Found 19 (27 requested) and removed 17 (13 requested) atoms. Cycle 2: After refmac, R = 0.2427 (Rfree = 0.000) for 3579 atoms. Found 5 (27 requested) and removed 18 (13 requested) atoms. Cycle 3: After refmac, R = 0.2376 (Rfree = 0.000) for 3535 atoms. Found 6 (26 requested) and removed 16 (13 requested) atoms. Cycle 4: After refmac, R = 0.2354 (Rfree = 0.000) for 3509 atoms. Found 4 (26 requested) and removed 15 (13 requested) atoms. Cycle 5: After refmac, R = 0.2338 (Rfree = 0.000) for 3492 atoms. Found 5 (26 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.45 Search for helices and strands: 0 residues in 0 chains, 3627 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 3641 seeds are put forward Round 1: 285 peptides, 37 chains. Longest chain 18 peptides. Score 0.575 Round 2: 326 peptides, 35 chains. Longest chain 30 peptides. Score 0.678 Round 3: 322 peptides, 35 chains. Longest chain 19 peptides. Score 0.671 Round 4: 327 peptides, 33 chains. Longest chain 20 peptides. Score 0.696 Round 5: 322 peptides, 30 chains. Longest chain 37 peptides. Score 0.712 Taking the results from Round 5 Chains 32, Residues 292, Estimated correctness of the model 60.9 % 2 chains (26 residues) have been docked in sequence Building loops using Loopy2018 32 chains (292 residues) following loop building 2 chains (26 residues) in sequence following loop building ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 7744 restraints for refining 3589 atoms. 6499 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2626 (Rfree = 0.000) for 3589 atoms. Found 15 (27 requested) and removed 24 (13 requested) atoms. Cycle 7: After refmac, R = 0.2428 (Rfree = 0.000) for 3555 atoms. Found 9 (26 requested) and removed 16 (13 requested) atoms. Cycle 8: After refmac, R = 0.2337 (Rfree = 0.000) for 3541 atoms. Found 1 (25 requested) and removed 14 (13 requested) atoms. Cycle 9: After refmac, R = 0.2301 (Rfree = 0.000) for 3524 atoms. Found 5 (24 requested) and removed 13 (13 requested) atoms. Cycle 10: After refmac, R = 0.2273 (Rfree = 0.000) for 3513 atoms. Found 1 (24 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.40 3.40 Search for helices and strands: 0 residues in 0 chains, 3616 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 3642 seeds are put forward Round 1: 272 peptides, 38 chains. Longest chain 25 peptides. Score 0.534 Round 2: 291 peptides, 38 chains. Longest chain 24 peptides. Score 0.579 Round 3: 291 peptides, 35 chains. Longest chain 21 peptides. Score 0.609 Round 4: 292 peptides, 34 chains. Longest chain 18 peptides. Score 0.620 Round 5: 302 peptides, 35 chains. Longest chain 27 peptides. Score 0.632 Taking the results from Round 5 Chains 35, Residues 267, Estimated correctness of the model 38.8 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8310 restraints for refining 3635 atoms. 7242 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2438 (Rfree = 0.000) for 3635 atoms. Found 20 (24 requested) and removed 18 (13 requested) atoms. Cycle 12: After refmac, R = 0.2251 (Rfree = 0.000) for 3631 atoms. Found 3 (24 requested) and removed 18 (13 requested) atoms. Cycle 13: After refmac, R = 0.2171 (Rfree = 0.000) for 3609 atoms. Found 8 (24 requested) and removed 15 (13 requested) atoms. Cycle 14: After refmac, R = 0.2088 (Rfree = 0.000) for 3589 atoms. Found 5 (24 requested) and removed 15 (13 requested) atoms. Cycle 15: After refmac, R = 0.2015 (Rfree = 0.000) for 3576 atoms. Found 1 (24 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.37 Search for helices and strands: 0 residues in 0 chains, 3715 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 3741 seeds are put forward Round 1: 260 peptides, 37 chains. Longest chain 19 peptides. Score 0.515 Round 2: 296 peptides, 38 chains. Longest chain 18 peptides. Score 0.590 Round 3: 318 peptides, 41 chains. Longest chain 19 peptides. Score 0.608 Round 4: 324 peptides, 38 chains. Longest chain 30 peptides. Score 0.648 Round 5: 316 peptides, 39 chains. Longest chain 20 peptides. Score 0.623 Taking the results from Round 4 Chains 41, Residues 286, Estimated correctness of the model 43.6 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8026 restraints for refining 3637 atoms. 6839 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2366 (Rfree = 0.000) for 3637 atoms. Found 13 (24 requested) and removed 18 (13 requested) atoms. Cycle 17: After refmac, R = 0.2231 (Rfree = 0.000) for 3616 atoms. Found 7 (24 requested) and removed 18 (13 requested) atoms. Cycle 18: After refmac, R = 0.2108 (Rfree = 0.000) for 3595 atoms. Found 4 (24 requested) and removed 14 (13 requested) atoms. Cycle 19: After refmac, R = 0.2076 (Rfree = 0.000) for 3578 atoms. Found 3 (24 requested) and removed 13 (13 requested) atoms. Cycle 20: After refmac, R = 0.2063 (Rfree = 0.000) for 3566 atoms. Found 5 (23 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.39 Search for helices and strands: 0 residues in 0 chains, 3659 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 3689 seeds are put forward Round 1: 272 peptides, 43 chains. Longest chain 17 peptides. Score 0.478 Round 2: 288 peptides, 37 chains. Longest chain 25 peptides. Score 0.582 Round 3: 309 peptides, 37 chains. Longest chain 21 peptides. Score 0.627 Round 4: 303 peptides, 37 chains. Longest chain 25 peptides. Score 0.615 Round 5: 296 peptides, 35 chains. Longest chain 19 peptides. Score 0.619 Taking the results from Round 3 Chains 38, Residues 272, Estimated correctness of the model 37.2 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8081 restraints for refining 3637 atoms. 6996 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2196 (Rfree = 0.000) for 3637 atoms. Found 7 (24 requested) and removed 14 (13 requested) atoms. Cycle 22: After refmac, R = 0.1988 (Rfree = 0.000) for 3618 atoms. Found 3 (24 requested) and removed 15 (13 requested) atoms. Cycle 23: After refmac, R = 0.1979 (Rfree = 0.000) for 3599 atoms. Found 1 (24 requested) and removed 14 (13 requested) atoms. Cycle 24: After refmac, R = 0.1981 (Rfree = 0.000) for 3580 atoms. Found 4 (24 requested) and removed 14 (13 requested) atoms. Cycle 25: After refmac, R = 0.1978 (Rfree = 0.000) for 3566 atoms. Found 2 (23 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.38 Search for helices and strands: 0 residues in 0 chains, 3665 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 3694 seeds are put forward Round 1: 274 peptides, 42 chains. Longest chain 15 peptides. Score 0.494 Round 2: 303 peptides, 39 chains. Longest chain 24 peptides. Score 0.595 Round 3: 302 peptides, 36 chains. Longest chain 23 peptides. Score 0.622 Round 4: 306 peptides, 34 chains. Longest chain 24 peptides. Score 0.649 Round 5: 296 peptides, 36 chains. Longest chain 21 peptides. Score 0.610 Taking the results from Round 4 Chains 37, Residues 272, Estimated correctness of the model 43.8 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 7827 restraints for refining 3637 atoms. 6670 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2197 (Rfree = 0.000) for 3637 atoms. Found 7 (24 requested) and removed 17 (13 requested) atoms. Cycle 27: After refmac, R = 0.2035 (Rfree = 0.000) for 3612 atoms. Found 6 (24 requested) and removed 15 (13 requested) atoms. Cycle 28: After refmac, R = 0.2181 (Rfree = 0.000) for 3601 atoms. Found 6 (24 requested) and removed 16 (13 requested) atoms. Cycle 29: After refmac, R = 0.1944 (Rfree = 0.000) for 3586 atoms. Found 5 (24 requested) and removed 15 (13 requested) atoms. Cycle 30: After refmac, R = 0.1965 (Rfree = 0.000) for 3561 atoms. Found 3 (24 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.41 Search for helices and strands: 0 residues in 0 chains, 3682 seeds are put forward NCS extension: 20 residues added (7 deleted due to clashes), 3702 seeds are put forward Round 1: 254 peptides, 40 chains. Longest chain 14 peptides. Score 0.464 Round 2: 285 peptides, 33 chains. Longest chain 19 peptides. Score 0.615 Round 3: 290 peptides, 31 chains. Longest chain 35 peptides. Score 0.645 Round 4: 277 peptides, 38 chains. Longest chain 18 peptides. Score 0.546 Round 5: 263 peptides, 35 chains. Longest chain 16 peptides. Score 0.544 Taking the results from Round 3 Chains 31, Residues 259, Estimated correctness of the model 42.7 % 1 chains (34 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 7833 restraints for refining 3636 atoms. 6679 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2296 (Rfree = 0.000) for 3636 atoms. Found 20 (24 requested) and removed 25 (13 requested) atoms. Cycle 32: After refmac, R = 0.2212 (Rfree = 0.000) for 3619 atoms. Found 6 (24 requested) and removed 14 (13 requested) atoms. Cycle 33: After refmac, R = 0.2158 (Rfree = 0.000) for 3607 atoms. Found 5 (24 requested) and removed 15 (13 requested) atoms. Cycle 34: After refmac, R = 0.2019 (Rfree = 0.000) for 3586 atoms. Found 4 (24 requested) and removed 15 (13 requested) atoms. Cycle 35: After refmac, R = 0.2269 (Rfree = 0.000) for 3564 atoms. Found 23 (23 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.37 Search for helices and strands: 0 residues in 0 chains, 3700 seeds are put forward NCS extension: 43 residues added (6 deleted due to clashes), 3743 seeds are put forward Round 1: 264 peptides, 38 chains. Longest chain 16 peptides. Score 0.514 Round 2: 285 peptides, 36 chains. Longest chain 22 peptides. Score 0.585 Round 3: 302 peptides, 36 chains. Longest chain 25 peptides. Score 0.622 Round 4: 299 peptides, 38 chains. Longest chain 25 peptides. Score 0.596 Round 5: 292 peptides, 37 chains. Longest chain 30 peptides. Score 0.591 Taking the results from Round 3 Chains 39, Residues 266, Estimated correctness of the model 35.7 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8000 restraints for refining 3636 atoms. 6877 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2271 (Rfree = 0.000) for 3636 atoms. Found 11 (24 requested) and removed 15 (13 requested) atoms. Cycle 37: After refmac, R = 0.2149 (Rfree = 0.000) for 3621 atoms. Found 2 (24 requested) and removed 13 (13 requested) atoms. Cycle 38: After refmac, R = 0.2088 (Rfree = 0.000) for 3609 atoms. Found 4 (24 requested) and removed 13 (13 requested) atoms. Cycle 39: After refmac, R = 0.2250 (Rfree = 0.000) for 3596 atoms. Found 11 (24 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.2095 (Rfree = 0.000) for 3581 atoms. Found 1 (24 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.37 Search for helices and strands: 0 residues in 0 chains, 3660 seeds are put forward NCS extension: 32 residues added (5 deleted due to clashes), 3692 seeds are put forward Round 1: 238 peptides, 38 chains. Longest chain 20 peptides. Score 0.444 Round 2: 269 peptides, 36 chains. Longest chain 23 peptides. Score 0.548 Round 3: 272 peptides, 34 chains. Longest chain 23 peptides. Score 0.576 Round 4: 269 peptides, 35 chains. Longest chain 24 peptides. Score 0.559 Round 5: 270 peptides, 33 chains. Longest chain 24 peptides. Score 0.582 Taking the results from Round 5 Chains 34, Residues 237, Estimated correctness of the model 22.7 % 3 chains (36 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8105 restraints for refining 3637 atoms. 7057 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2288 (Rfree = 0.000) for 3637 atoms. Found 11 (24 requested) and removed 26 (13 requested) atoms. Cycle 42: After refmac, R = 0.2753 (Rfree = 0.000) for 3616 atoms. Found 20 (24 requested) and removed 20 (13 requested) atoms. Cycle 43: After refmac, R = 0.2579 (Rfree = 0.000) for 3608 atoms. Found 20 (24 requested) and removed 20 (13 requested) atoms. Cycle 44: After refmac, R = 0.2059 (Rfree = 0.000) for 3602 atoms. Found 5 (24 requested) and removed 16 (13 requested) atoms. Cycle 45: After refmac, R = 0.2025 (Rfree = 0.000) for 3586 atoms. Found 8 (24 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.38 Search for helices and strands: 0 residues in 0 chains, 3681 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 3711 seeds are put forward Round 1: 220 peptides, 37 chains. Longest chain 13 peptides. Score 0.405 Round 2: 244 peptides, 34 chains. Longest chain 25 peptides. Score 0.508 Round 3: 238 peptides, 32 chains. Longest chain 16 peptides. Score 0.516 Round 4: 246 peptides, 33 chains. Longest chain 21 peptides. Score 0.525 Round 5: 249 peptides, 34 chains. Longest chain 15 peptides. Score 0.521 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 213, Estimated correctness of the model 2.3 % 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. 7942 reflections ( 99.75 % complete ) and 8675 restraints for refining 3636 atoms. 7856 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2247 (Rfree = 0.000) for 3636 atoms. Found 0 (24 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.2125 (Rfree = 0.000) for 3611 atoms. Found 0 (24 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.2544 (Rfree = 0.000) for 3594 atoms. Found 0 (24 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.2070 (Rfree = 0.000) for 3573 atoms. TimeTaking 55.03