Mon 24 Dec 07:32:02 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p7i-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p7i-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p7i-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.2-parrot-noncs ############### 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 07:32:06 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/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p7i-3.2-parrot-noncs/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 365 and 0 Target number of residues in the AU: 365 Target solvent content: 0.6386 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-3.2-parrot-noncs.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-3.2-parrot-noncs.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 3.200 Wilson plot Bfac: 71.18 9471 reflections ( 99.79 % complete ) and 0 restraints for refining 4436 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3171 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3254 (Rfree = 0.000) for 4436 atoms. Found 32 (39 requested) and removed 41 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.28 Search for helices and strands: 0 residues in 0 chains, 4480 seeds are put forward NCS extension: 0 residues added, 4480 seeds are put forward Round 1: 201 peptides, 39 chains. Longest chain 11 peptides. Score 0.321 Round 2: 263 peptides, 44 chains. Longest chain 12 peptides. Score 0.442 Round 3: 283 peptides, 41 chains. Longest chain 17 peptides. Score 0.528 Round 4: 299 peptides, 39 chains. Longest chain 18 peptides. Score 0.587 Round 5: 314 peptides, 38 chains. Longest chain 16 peptides. Score 0.628 Taking the results from Round 5 Chains 39, Residues 276, Estimated correctness of the model 48.4 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 8078 restraints for refining 3651 atoms. 6980 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2818 (Rfree = 0.000) for 3651 atoms. Found 17 (32 requested) and removed 34 (16 requested) atoms. Cycle 2: After refmac, R = 0.2702 (Rfree = 0.000) for 3586 atoms. Found 11 (32 requested) and removed 25 (16 requested) atoms. Cycle 3: After refmac, R = 0.2393 (Rfree = 0.000) for 3546 atoms. Found 10 (32 requested) and removed 19 (16 requested) atoms. Cycle 4: After refmac, R = 0.2349 (Rfree = 0.000) for 3521 atoms. Found 7 (31 requested) and removed 17 (15 requested) atoms. Cycle 5: After refmac, R = 0.2353 (Rfree = 0.000) for 3501 atoms. Found 7 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 3.32 Search for helices and strands: 0 residues in 0 chains, 3618 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 3634 seeds are put forward Round 1: 302 peptides, 39 chains. Longest chain 16 peptides. Score 0.593 Round 2: 312 peptides, 33 chains. Longest chain 26 peptides. Score 0.669 Round 3: 331 peptides, 33 chains. Longest chain 24 peptides. Score 0.703 Round 4: 338 peptides, 35 chains. Longest chain 30 peptides. Score 0.699 Round 5: 338 peptides, 37 chains. Longest chain 23 peptides. Score 0.683 Taking the results from Round 3 Chains 35, Residues 298, Estimated correctness of the model 65.8 % 4 chains (45 residues) have been docked in sequence Building loops using Loopy2018 35 chains (298 residues) following loop building 4 chains (45 residues) in sequence following loop building ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7368 restraints for refining 3610 atoms. 6020 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2705 (Rfree = 0.000) for 3610 atoms. Found 19 (32 requested) and removed 43 (16 requested) atoms. Cycle 7: After refmac, R = 0.2575 (Rfree = 0.000) for 3556 atoms. Found 13 (31 requested) and removed 25 (16 requested) atoms. Cycle 8: After refmac, R = 0.2526 (Rfree = 0.000) for 3520 atoms. Found 8 (30 requested) and removed 21 (15 requested) atoms. Cycle 9: After refmac, R = 0.2423 (Rfree = 0.000) for 3490 atoms. Found 5 (29 requested) and removed 19 (15 requested) atoms. Cycle 10: After refmac, R = 0.2261 (Rfree = 0.000) for 3470 atoms. Found 4 (29 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.28 3.28 Search for helices and strands: 0 residues in 0 chains, 3560 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 3573 seeds are put forward Round 1: 283 peptides, 37 chains. Longest chain 27 peptides. Score 0.571 Round 2: 334 peptides, 39 chains. Longest chain 28 peptides. Score 0.659 Round 3: 335 peptides, 37 chains. Longest chain 27 peptides. Score 0.678 Round 4: 337 peptides, 39 chains. Longest chain 26 peptides. Score 0.664 Round 5: 327 peptides, 32 chains. Longest chain 32 peptides. Score 0.705 Taking the results from Round 5 Chains 33, Residues 295, Estimated correctness of the model 66.2 % 4 chains (79 residues) have been docked in sequence Building loops using Loopy2018 33 chains (295 residues) following loop building 4 chains (79 residues) in sequence following loop building ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7176 restraints for refining 3651 atoms. 5676 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2690 (Rfree = 0.000) for 3651 atoms. Found 21 (29 requested) and removed 28 (16 requested) atoms. Cycle 12: After refmac, R = 0.2870 (Rfree = 0.000) for 3630 atoms. Found 22 (28 requested) and removed 22 (16 requested) atoms. Cycle 13: After refmac, R = 0.2473 (Rfree = 0.000) for 3609 atoms. Found 17 (28 requested) and removed 25 (16 requested) atoms. Cycle 14: After refmac, R = 0.2186 (Rfree = 0.000) for 3594 atoms. Found 8 (27 requested) and removed 22 (16 requested) atoms. Cycle 15: After refmac, R = 0.2112 (Rfree = 0.000) for 3576 atoms. Found 3 (26 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.26 Search for helices and strands: 0 residues in 0 chains, 3669 seeds are put forward NCS extension: 31 residues added (14 deleted due to clashes), 3700 seeds are put forward Round 1: 306 peptides, 38 chains. Longest chain 24 peptides. Score 0.612 Round 2: 336 peptides, 40 chains. Longest chain 25 peptides. Score 0.654 Round 3: 340 peptides, 36 chains. Longest chain 26 peptides. Score 0.695 Round 4: 344 peptides, 33 chains. Longest chain 31 peptides. Score 0.725 Round 5: 319 peptides, 38 chains. Longest chain 23 peptides. Score 0.638 Taking the results from Round 4 Chains 35, Residues 311, Estimated correctness of the model 70.3 % 2 chains (25 residues) have been docked in sequence Building loops using Loopy2018 35 chains (311 residues) following loop building 2 chains (25 residues) in sequence following loop building ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7799 restraints for refining 3652 atoms. 6487 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2420 (Rfree = 0.000) for 3652 atoms. Found 16 (26 requested) and removed 23 (16 requested) atoms. Cycle 17: After refmac, R = 0.2229 (Rfree = 0.000) for 3634 atoms. Found 11 (25 requested) and removed 21 (16 requested) atoms. Cycle 18: After refmac, R = 0.2163 (Rfree = 0.000) for 3612 atoms. Found 6 (24 requested) and removed 20 (16 requested) atoms. Cycle 19: After refmac, R = 0.2140 (Rfree = 0.000) for 3591 atoms. Found 7 (24 requested) and removed 17 (16 requested) atoms. Cycle 20: After refmac, R = 0.2076 (Rfree = 0.000) for 3575 atoms. Found 0 (23 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.28 Search for helices and strands: 0 residues in 0 chains, 3664 seeds are put forward NCS extension: 12 residues added (10 deleted due to clashes), 3676 seeds are put forward Round 1: 307 peptides, 43 chains. Longest chain 18 peptides. Score 0.564 Round 2: 323 peptides, 36 chains. Longest chain 31 peptides. Score 0.664 Round 3: 329 peptides, 36 chains. Longest chain 22 peptides. Score 0.675 Round 4: 332 peptides, 34 chains. Longest chain 32 peptides. Score 0.697 Round 5: 318 peptides, 34 chains. Longest chain 40 peptides. Score 0.672 Taking the results from Round 4 Chains 34, Residues 298, Estimated correctness of the model 64.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 8081 restraints for refining 3652 atoms. 6923 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2359 (Rfree = 0.000) for 3652 atoms. Found 13 (22 requested) and removed 17 (16 requested) atoms. Cycle 22: After refmac, R = 0.2496 (Rfree = 0.000) for 3642 atoms. Found 12 (22 requested) and removed 17 (16 requested) atoms. Cycle 23: After refmac, R = 0.2306 (Rfree = 0.000) for 3632 atoms. Found 10 (22 requested) and removed 19 (16 requested) atoms. Cycle 24: After refmac, R = 0.2147 (Rfree = 0.000) for 3615 atoms. Found 6 (22 requested) and removed 18 (16 requested) atoms. Cycle 25: After refmac, R = 0.2234 (Rfree = 0.000) for 3601 atoms. Found 11 (22 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.27 Search for helices and strands: 0 residues in 0 chains, 3708 seeds are put forward NCS extension: 23 residues added (7 deleted due to clashes), 3731 seeds are put forward Round 1: 274 peptides, 39 chains. Longest chain 16 peptides. Score 0.528 Round 2: 318 peptides, 32 chains. Longest chain 26 peptides. Score 0.689 Round 3: 333 peptides, 36 chains. Longest chain 24 peptides. Score 0.682 Round 4: 331 peptides, 36 chains. Longest chain 28 peptides. Score 0.679 Round 5: 313 peptides, 35 chains. Longest chain 25 peptides. Score 0.654 Taking the results from Round 2 Chains 33, Residues 286, Estimated correctness of the model 62.8 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7685 restraints for refining 3651 atoms. 6465 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2391 (Rfree = 0.000) for 3651 atoms. Found 11 (22 requested) and removed 17 (16 requested) atoms. Cycle 27: After refmac, R = 0.2545 (Rfree = 0.000) for 3634 atoms. Found 20 (22 requested) and removed 22 (16 requested) atoms. Cycle 28: After refmac, R = 0.2196 (Rfree = 0.000) for 3621 atoms. Found 6 (22 requested) and removed 17 (16 requested) atoms. Cycle 29: After refmac, R = 0.2146 (Rfree = 0.000) for 3602 atoms. Found 3 (22 requested) and removed 17 (16 requested) atoms. Cycle 30: After refmac, R = 0.2135 (Rfree = 0.000) for 3581 atoms. Found 4 (22 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.28 Search for helices and strands: 0 residues in 0 chains, 3687 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3706 seeds are put forward Round 1: 282 peptides, 43 chains. Longest chain 23 peptides. Score 0.504 Round 2: 305 peptides, 30 chains. Longest chain 26 peptides. Score 0.682 Round 3: 298 peptides, 35 chains. Longest chain 20 peptides. Score 0.623 Round 4: 314 peptides, 35 chains. Longest chain 21 peptides. Score 0.656 Round 5: 299 peptides, 33 chains. Longest chain 26 peptides. Score 0.644 Taking the results from Round 2 Chains 31, Residues 275, Estimated correctness of the model 61.3 % 3 chains (32 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7530 restraints for refining 3640 atoms. 6334 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2264 (Rfree = 0.000) for 3640 atoms. Found 13 (22 requested) and removed 22 (16 requested) atoms. Cycle 32: After refmac, R = 0.2236 (Rfree = 0.000) for 3619 atoms. Found 7 (22 requested) and removed 20 (16 requested) atoms. Cycle 33: After refmac, R = 0.2436 (Rfree = 0.000) for 3594 atoms. Found 22 (22 requested) and removed 23 (16 requested) atoms. Cycle 34: After refmac, R = 0.2237 (Rfree = 0.000) for 3581 atoms. Found 15 (22 requested) and removed 22 (16 requested) atoms. Cycle 35: After refmac, R = 0.2075 (Rfree = 0.000) for 3570 atoms. Found 6 (22 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.27 3.27 Search for helices and strands: 0 residues in 0 chains, 3665 seeds are put forward NCS extension: 26 residues added (7 deleted due to clashes), 3691 seeds are put forward Round 1: 262 peptides, 36 chains. Longest chain 17 peptides. Score 0.531 Round 2: 285 peptides, 36 chains. Longest chain 17 peptides. Score 0.585 Round 3: 294 peptides, 34 chains. Longest chain 26 peptides. Score 0.625 Round 4: 285 peptides, 36 chains. Longest chain 17 peptides. Score 0.585 Round 5: 286 peptides, 38 chains. Longest chain 19 peptides. Score 0.567 Taking the results from Round 3 Chains 34, Residues 260, Estimated correctness of the model 47.6 % 3 chains (45 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7655 restraints for refining 3652 atoms. 6470 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2351 (Rfree = 0.000) for 3652 atoms. Found 15 (22 requested) and removed 19 (16 requested) atoms. Cycle 37: After refmac, R = 0.2279 (Rfree = 0.000) for 3633 atoms. Found 16 (22 requested) and removed 18 (16 requested) atoms. Cycle 38: After refmac, R = 0.2211 (Rfree = 0.000) for 3617 atoms. Found 6 (22 requested) and removed 16 (16 requested) atoms. Cycle 39: After refmac, R = 0.2401 (Rfree = 0.000) for 3602 atoms. Found 22 (22 requested) and removed 17 (16 requested) atoms. Cycle 40: After refmac, R = 0.2141 (Rfree = 0.000) for 3597 atoms. Found 6 (22 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.28 3.28 Search for helices and strands: 0 residues in 0 chains, 3693 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 3710 seeds are put forward Round 1: 264 peptides, 38 chains. Longest chain 17 peptides. Score 0.514 Round 2: 297 peptides, 33 chains. Longest chain 19 peptides. Score 0.640 Round 3: 305 peptides, 34 chains. Longest chain 19 peptides. Score 0.647 Round 4: 295 peptides, 33 chains. Longest chain 22 peptides. Score 0.636 Round 5: 298 peptides, 31 chains. Longest chain 22 peptides. Score 0.660 Taking the results from Round 5 Chains 33, Residues 267, Estimated correctness of the model 56.2 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 9471 reflections ( 99.79 % complete ) and 7650 restraints for refining 3650 atoms. 6454 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2427 (Rfree = 0.000) for 3650 atoms. Found 13 (22 requested) and removed 20 (16 requested) atoms. Cycle 42: After refmac, R = 0.2376 (Rfree = 0.000) for 3626 atoms. Found 7 (22 requested) and removed 20 (16 requested) atoms. Cycle 43: After refmac, R = 0.2337 (Rfree = 0.000) for 3595 atoms. Found 15 (22 requested) and removed 19 (16 requested) atoms. Cycle 44: After refmac, R = 0.2274 (Rfree = 0.000) for 3580 atoms. Found 9 (22 requested) and removed 18 (16 requested) atoms. Cycle 45: After refmac, R = 0.2245 (Rfree = 0.000) for 3560 atoms. Found 11 (22 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.27 3.27 Search for helices and strands: 0 residues in 0 chains, 3651 seeds are put forward NCS extension: 9 residues added (15 deleted due to clashes), 3660 seeds are put forward Round 1: 239 peptides, 40 chains. Longest chain 14 peptides. Score 0.423 Round 2: 262 peptides, 36 chains. Longest chain 17 peptides. Score 0.531 Round 3: 268 peptides, 33 chains. Longest chain 26 peptides. Score 0.578 Round 4: 287 peptides, 36 chains. Longest chain 23 peptides. Score 0.590 Round 5: 282 peptides, 37 chains. Longest chain 24 peptides. Score 0.568 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 251, Estimated correctness of the model 38.3 % 2 chains (31 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2p7i-3_warpNtrace.pdb as input Building loops using Loopy2018 38 chains (251 residues) following loop building 2 chains (31 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9471 reflections ( 99.79 % complete ) and 7413 restraints for refining 3511 atoms. 6331 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2394 (Rfree = 0.000) for 3511 atoms. Found 0 (22 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2377 (Rfree = 0.000) for 3491 atoms. Found 0 (22 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.2330 (Rfree = 0.000) for 3468 atoms. Found 0 (22 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.2573 (Rfree = 0.000) for 3450 atoms. TimeTaking 50.1