Sun 23 Dec 22:23:05 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p7i-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p7i-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.4-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 22:23:15 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p7i-3.4-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 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-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-3.4-parrot-hancs.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 4439 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3187 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3062 (Rfree = 0.000) for 4439 atoms. Found 23 (33 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.48 3.48 Search for helices and strands: 0 residues in 0 chains, 4538 seeds are put forward NCS extension: 0 residues added, 4538 seeds are put forward Round 1: 224 peptides, 40 chains. Longest chain 11 peptides. Score 0.379 Round 2: 283 peptides, 37 chains. Longest chain 19 peptides. Score 0.571 Round 3: 295 peptides, 35 chains. Longest chain 24 peptides. Score 0.617 Round 4: 306 peptides, 38 chains. Longest chain 19 peptides. Score 0.612 Round 5: 307 peptides, 32 chains. Longest chain 30 peptides. Score 0.669 Taking the results from Round 5 Chains 36, Residues 275, Estimated correctness of the model 49.6 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 7934 restraints for refining 3637 atoms. 6776 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2523 (Rfree = 0.000) for 3637 atoms. Found 21 (27 requested) and removed 31 (13 requested) atoms. Cycle 2: After refmac, R = 0.2301 (Rfree = 0.000) for 3586 atoms. Found 11 (27 requested) and removed 18 (13 requested) atoms. Cycle 3: After refmac, R = 0.2193 (Rfree = 0.000) for 3566 atoms. Found 3 (27 requested) and removed 17 (13 requested) atoms. Cycle 4: After refmac, R = 0.2336 (Rfree = 0.000) for 3540 atoms. Found 9 (26 requested) and removed 20 (13 requested) atoms. Cycle 5: After refmac, R = 0.2231 (Rfree = 0.000) for 3513 atoms. Found 10 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.42 3.42 Search for helices and strands: 0 residues in 0 chains, 3663 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 3683 seeds are put forward Round 1: 293 peptides, 40 chains. Longest chain 16 peptides. Score 0.563 Round 2: 317 peptides, 36 chains. Longest chain 24 peptides. Score 0.652 Round 3: 308 peptides, 36 chains. Longest chain 23 peptides. Score 0.635 Round 4: 304 peptides, 36 chains. Longest chain 21 peptides. Score 0.626 Round 5: 296 peptides, 37 chains. Longest chain 22 peptides. Score 0.600 Taking the results from Round 2 Chains 38, Residues 281, Estimated correctness of the model 44.7 % 2 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 7573 restraints for refining 3579 atoms. 6365 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2290 (Rfree = 0.000) for 3579 atoms. Found 10 (27 requested) and removed 35 (13 requested) atoms. Cycle 7: After refmac, R = 0.2098 (Rfree = 0.000) for 3529 atoms. Found 5 (26 requested) and removed 16 (13 requested) atoms. Cycle 8: After refmac, R = 0.2072 (Rfree = 0.000) for 3509 atoms. Found 6 (26 requested) and removed 18 (13 requested) atoms. Cycle 9: After refmac, R = 0.2024 (Rfree = 0.000) for 3489 atoms. Found 6 (26 requested) and removed 22 (13 requested) atoms. Cycle 10: After refmac, R = 0.2150 (Rfree = 0.000) for 3462 atoms. Found 10 (26 requested) and removed 21 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.37 3.37 Search for helices and strands: 0 residues in 0 chains, 3575 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3593 seeds are put forward Round 1: 291 peptides, 41 chains. Longest chain 28 peptides. Score 0.547 Round 2: 306 peptides, 37 chains. Longest chain 21 peptides. Score 0.621 Round 3: 297 peptides, 41 chains. Longest chain 19 peptides. Score 0.562 Round 4: 304 peptides, 37 chains. Longest chain 23 peptides. Score 0.617 Round 5: 302 peptides, 39 chains. Longest chain 22 peptides. Score 0.593 Taking the results from Round 2 Chains 39, Residues 269, Estimated correctness of the model 35.4 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 7806 restraints for refining 3635 atoms. 6677 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2297 (Rfree = 0.000) for 3635 atoms. Found 8 (27 requested) and removed 72 (13 requested) atoms. Cycle 12: After refmac, R = 0.2140 (Rfree = 0.000) for 3553 atoms. Found 8 (26 requested) and removed 21 (13 requested) atoms. Cycle 13: After refmac, R = 0.2053 (Rfree = 0.000) for 3532 atoms. Found 6 (26 requested) and removed 16 (13 requested) atoms. Cycle 14: After refmac, R = 0.2398 (Rfree = 0.000) for 3515 atoms. Found 26 (26 requested) and removed 16 (13 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2159 (Rfree = 0.000) for 3519 atoms. Found 8 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.36 Search for helices and strands: 0 residues in 0 chains, 3624 seeds are put forward NCS extension: 17 residues added (5 deleted due to clashes), 3641 seeds are put forward Round 1: 279 peptides, 42 chains. Longest chain 19 peptides. Score 0.507 Round 2: 295 peptides, 39 chains. Longest chain 19 peptides. Score 0.578 Round 3: 297 peptides, 36 chains. Longest chain 24 peptides. Score 0.612 Round 4: 299 peptides, 39 chains. Longest chain 18 peptides. Score 0.587 Round 5: 313 peptides, 38 chains. Longest chain 35 peptides. Score 0.626 Taking the results from Round 5 Chains 38, Residues 275, Estimated correctness of the model 36.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8154 restraints for refining 3634 atoms. 7092 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2284 (Rfree = 0.000) for 3634 atoms. Found 9 (27 requested) and removed 19 (13 requested) atoms. Cycle 17: After refmac, R = 0.2698 (Rfree = 0.000) for 3606 atoms. Found 27 (27 requested) and removed 23 (13 requested) atoms. Cycle 18: After refmac, R = 0.2311 (Rfree = 0.000) for 3589 atoms. Found 11 (27 requested) and removed 18 (13 requested) atoms. Cycle 19: After refmac, R = 0.2764 (Rfree = 0.000) for 3564 atoms. Found 27 (27 requested) and removed 20 (13 requested) atoms. Cycle 20: After refmac, R = 0.2093 (Rfree = 0.000) for 3559 atoms. Found 7 (26 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.37 3.37 Search for helices and strands: 0 residues in 0 chains, 3695 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 3722 seeds are put forward Round 1: 260 peptides, 45 chains. Longest chain 15 peptides. Score 0.421 Round 2: 298 peptides, 43 chains. Longest chain 16 peptides. Score 0.543 Round 3: 301 peptides, 42 chains. Longest chain 20 peptides. Score 0.561 Round 4: 278 peptides, 40 chains. Longest chain 14 peptides. Score 0.527 Round 5: 295 peptides, 44 chains. Longest chain 13 peptides. Score 0.525 Taking the results from Round 3 Chains 42, Residues 259, Estimated correctness of the model 15.4 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8209 restraints for refining 3628 atoms. 7195 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2354 (Rfree = 0.000) for 3628 atoms. Found 16 (27 requested) and removed 38 (13 requested) atoms. Cycle 22: After refmac, R = 0.2485 (Rfree = 0.000) for 3594 atoms. Found 16 (27 requested) and removed 20 (13 requested) atoms. Cycle 23: After refmac, R = 0.2417 (Rfree = 0.000) for 3577 atoms. Found 18 (27 requested) and removed 21 (13 requested) atoms. Cycle 24: After refmac, R = 0.2572 (Rfree = 0.000) for 3561 atoms. Found 26 (26 requested) and removed 29 (13 requested) atoms. Cycle 25: After refmac, R = 0.2409 (Rfree = 0.000) for 3546 atoms. Found 26 (26 requested) and removed 27 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.33 Search for helices and strands: 0 residues in 0 chains, 3687 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3703 seeds are put forward Round 1: 226 peptides, 43 chains. Longest chain 12 peptides. Score 0.346 Round 2: 256 peptides, 44 chains. Longest chain 13 peptides. Score 0.422 Round 3: 265 peptides, 40 chains. Longest chain 14 peptides. Score 0.494 Round 4: 267 peptides, 42 chains. Longest chain 14 peptides. Score 0.476 Round 5: 265 peptides, 38 chains. Longest chain 25 peptides. Score 0.516 Taking the results from Round 5 Chains 0, Residues 0, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8246 restraints for refining 3635 atoms. 7376 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2238 (Rfree = 0.000) for 3635 atoms. Found 10 (27 requested) and removed 18 (13 requested) atoms. Cycle 27: After refmac, R = 0.2158 (Rfree = 0.000) for 3610 atoms. Found 20 (27 requested) and removed 16 (13 requested) atoms. Cycle 28: After refmac, R = 0.2146 (Rfree = 0.000) for 3604 atoms. Found 10 (27 requested) and removed 18 (13 requested) atoms. Cycle 29: After refmac, R = 0.2256 (Rfree = 0.000) for 3580 atoms. Found 22 (27 requested) and removed 16 (13 requested) atoms. Cycle 30: After refmac, R = 0.2473 (Rfree = 0.000) for 3580 atoms. Found 27 (27 requested) and removed 16 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 3.34 Search for helices and strands: 0 residues in 0 chains, 3732 seeds are put forward NCS extension: 35 residues added (2 deleted due to clashes), 3767 seeds are put forward Round 1: 238 peptides, 45 chains. Longest chain 11 peptides. Score 0.357 Round 2: 271 peptides, 39 chains. Longest chain 25 peptides. Score 0.520 Round 3: 293 peptides, 41 chains. Longest chain 23 peptides. Score 0.552 Round 4: 272 peptides, 38 chains. Longest chain 23 peptides. Score 0.534 Round 5: 272 peptides, 44 chains. Longest chain 11 peptides. Score 0.466 Taking the results from Round 3 Chains 41, Residues 252, Estimated correctness of the model 12.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8184 restraints for refining 3636 atoms. 7217 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2084 (Rfree = 0.000) for 3636 atoms. Found 13 (27 requested) and removed 15 (13 requested) atoms. Cycle 32: After refmac, R = 0.2305 (Rfree = 0.000) for 3615 atoms. Found 23 (27 requested) and removed 15 (13 requested) atoms. Cycle 33: After refmac, R = 0.2103 (Rfree = 0.000) for 3614 atoms. Found 17 (27 requested) and removed 16 (13 requested) atoms. Cycle 34: After refmac, R = 0.1753 (Rfree = 0.000) for 3609 atoms. Found 1 (27 requested) and removed 14 (13 requested) atoms. Cycle 35: After refmac, R = 0.1734 (Rfree = 0.000) for 3593 atoms. Found 4 (27 requested) and removed 15 (13 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.42 Search for helices and strands: 0 residues in 0 chains, 3709 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3731 seeds are put forward Round 1: 229 peptides, 45 chains. Longest chain 9 peptides. Score 0.329 Round 2: 273 peptides, 42 chains. Longest chain 19 peptides. Score 0.492 Round 3: 265 peptides, 37 chains. Longest chain 19 peptides. Score 0.527 Round 4: 266 peptides, 36 chains. Longest chain 19 peptides. Score 0.541 Round 5: 261 peptides, 35 chains. Longest chain 21 peptides. Score 0.539 Taking the results from Round 4 Chains 38, Residues 230, Estimated correctness of the model 8.3 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8197 restraints for refining 3635 atoms. 7245 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2257 (Rfree = 0.000) for 3635 atoms. Found 18 (27 requested) and removed 16 (13 requested) atoms. Cycle 37: After refmac, R = 0.2072 (Rfree = 0.000) for 3629 atoms. Found 9 (27 requested) and removed 15 (13 requested) atoms. Cycle 38: After refmac, R = 0.2205 (Rfree = 0.000) for 3620 atoms. Found 10 (27 requested) and removed 14 (13 requested) atoms. Cycle 39: After refmac, R = 0.2182 (Rfree = 0.000) for 3609 atoms. Found 17 (27 requested) and removed 13 (13 requested) atoms. Cycle 40: After refmac, R = 0.1831 (Rfree = 0.000) for 3604 atoms. Found 4 (27 requested) and removed 14 (13 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.35 Search for helices and strands: 0 residues in 0 chains, 3701 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3717 seeds are put forward Round 1: 206 peptides, 37 chains. Longest chain 10 peptides. Score 0.363 Round 2: 225 peptides, 35 chains. Longest chain 16 peptides. Score 0.445 Round 3: 227 peptides, 33 chains. Longest chain 15 peptides. Score 0.475 Round 4: 235 peptides, 36 chains. Longest chain 17 peptides. Score 0.460 Round 5: 254 peptides, 40 chains. Longest chain 17 peptides. Score 0.464 Taking the results from Round 3 Chains 33, Residues 194, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7942 reflections ( 99.75 % complete ) and 8415 restraints for refining 3637 atoms. 7641 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1987 (Rfree = 0.000) for 3637 atoms. Found 12 (27 requested) and removed 13 (13 requested) atoms. Cycle 42: After refmac, R = 0.1879 (Rfree = 0.000) for 3629 atoms. Found 3 (27 requested) and removed 13 (13 requested) atoms. Cycle 43: After refmac, R = 0.1817 (Rfree = 0.000) for 3616 atoms. Found 2 (27 requested) and removed 13 (13 requested) atoms. Cycle 44: After refmac, R = 0.1777 (Rfree = 0.000) for 3603 atoms. Found 2 (27 requested) and removed 13 (13 requested) atoms. Cycle 45: After refmac, R = 0.1769 (Rfree = 0.000) for 3591 atoms. Found 1 (27 requested) and removed 13 (13 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 3.41 Search for helices and strands: 0 residues in 0 chains, 3659 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 3678 seeds are put forward Round 1: 220 peptides, 40 chains. Longest chain 13 peptides. Score 0.367 Round 2: 236 peptides, 38 chains. Longest chain 14 peptides. Score 0.439 Round 3: 253 peptides, 37 chains. Longest chain 15 peptides. Score 0.497 Round 4: 241 peptides, 35 chains. Longest chain 15 peptides. Score 0.488 Round 5: 224 peptides, 33 chains. Longest chain 13 peptides. Score 0.467 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 216, 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. 7942 reflections ( 99.75 % complete ) and 8476 restraints for refining 3637 atoms. 7649 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2050 (Rfree = 0.000) for 3637 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 47: After refmac, R = 0.1960 (Rfree = 0.000) for 3623 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 48: After refmac, R = 0.1871 (Rfree = 0.000) for 3607 atoms. Found 0 (27 requested) and removed 13 (13 requested) atoms. Cycle 49: After refmac, R = 0.1792 (Rfree = 0.000) for 3589 atoms. TimeTaking 66.27