Mon 24 Dec 07:26:53 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 2pbl-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pbl-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pbl-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.8-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/2pbl-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.8-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 07:26:58 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/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-3.8-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 656 and 0 Target number of residues in the AU: 656 Target solvent content: 0.6484 Checking the provided sequence file Detected sequence length: 262 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1048 Adjusted target solvent content: 0.44 Input MTZ file: 2pbl-3.8-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: 4 Cell parameters: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 8384 target number of atoms Had to go as low as 0.75 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: 87.858 3.800 Wilson plot Bfac: 77.07 9891 reflections ( 98.93 % complete ) and 0 restraints for refining 9321 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3618 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4033 (Rfree = 0.000) for 9321 atoms. Found 51 (51 requested) and removed 227 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.74 Search for helices and strands: 0 residues in 0 chains, 9326 seeds are put forward NCS extension: 0 residues added, 9326 seeds are put forward Round 1: 255 peptides, 59 chains. Longest chain 7 peptides. Score 0.206 Round 2: 371 peptides, 78 chains. Longest chain 12 peptides. Score 0.277 Round 3: 413 peptides, 76 chains. Longest chain 11 peptides. Score 0.363 Round 4: 421 peptides, 79 chains. Longest chain 9 peptides. Score 0.355 Round 5: 457 peptides, 81 chains. Longest chain 14 peptides. Score 0.399 Taking the results from Round 5 Chains 83, Residues 376, Estimated correctness of the model 0.0 % 13 chains (66 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 17696 restraints for refining 7580 atoms. 16122 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3535 (Rfree = 0.000) for 7580 atoms. Found 41 (41 requested) and removed 99 (20 requested) atoms. Cycle 2: After refmac, R = 0.3497 (Rfree = 0.000) for 7319 atoms. Found 41 (41 requested) and removed 64 (20 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.3463 (Rfree = 0.000) for 7198 atoms. Found 40 (40 requested) and removed 48 (20 requested) atoms. Cycle 4: After refmac, R = 0.3481 (Rfree = 0.000) for 7090 atoms. Found 39 (39 requested) and removed 42 (19 requested) atoms. Cycle 5: After refmac, R = 0.3336 (Rfree = 0.000) for 7045 atoms. Found 38 (38 requested) and removed 36 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.75 Search for helices and strands: 0 residues in 0 chains, 7368 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 7390 seeds are put forward Round 1: 373 peptides, 77 chains. Longest chain 11 peptides. Score 0.287 Round 2: 463 peptides, 83 chains. Longest chain 13 peptides. Score 0.395 Round 3: 479 peptides, 83 chains. Longest chain 12 peptides. Score 0.420 Round 4: 474 peptides, 78 chains. Longest chain 12 peptides. Score 0.445 Round 5: 494 peptides, 82 chains. Longest chain 12 peptides. Score 0.449 Taking the results from Round 5 Chains 82, Residues 412, Estimated correctness of the model 0.0 % 13 chains (58 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 15871 restraints for refining 7145 atoms. 14187 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3240 (Rfree = 0.000) for 7145 atoms. Found 39 (39 requested) and removed 103 (19 requested) atoms. Cycle 7: After refmac, R = 0.2999 (Rfree = 0.000) for 6987 atoms. Found 38 (38 requested) and removed 50 (19 requested) atoms. Cycle 8: After refmac, R = 0.2905 (Rfree = 0.000) for 6895 atoms. Found 38 (38 requested) and removed 49 (19 requested) atoms. Cycle 9: After refmac, R = 0.2868 (Rfree = 0.000) for 6844 atoms. Found 37 (37 requested) and removed 33 (18 requested) atoms. Cycle 10: After refmac, R = 0.2792 (Rfree = 0.000) for 6819 atoms. Found 37 (37 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.80 Search for helices and strands: 0 residues in 0 chains, 7140 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 7152 seeds are put forward Round 1: 392 peptides, 78 chains. Longest chain 10 peptides. Score 0.313 Round 2: 468 peptides, 78 chains. Longest chain 18 peptides. Score 0.436 Round 3: 479 peptides, 76 chains. Longest chain 17 peptides. Score 0.465 Round 4: 515 peptides, 82 chains. Longest chain 18 peptides. Score 0.480 Round 5: 506 peptides, 75 chains. Longest chain 15 peptides. Score 0.510 Taking the results from Round 5 Chains 76, Residues 431, Estimated correctness of the model 0.0 % 9 chains (60 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 15894 restraints for refining 7218 atoms. 14056 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2966 (Rfree = 0.000) for 7218 atoms. Found 39 (39 requested) and removed 77 (19 requested) atoms. Cycle 12: After refmac, R = 0.2813 (Rfree = 0.000) for 7086 atoms. Found 39 (39 requested) and removed 67 (19 requested) atoms. Cycle 13: After refmac, R = 0.2809 (Rfree = 0.000) for 7011 atoms. Found 38 (38 requested) and removed 44 (19 requested) atoms. Cycle 14: After refmac, R = 0.2704 (Rfree = 0.000) for 6952 atoms. Found 38 (38 requested) and removed 38 (19 requested) atoms. Cycle 15: After refmac, R = 0.2730 (Rfree = 0.000) for 6924 atoms. Found 38 (38 requested) and removed 37 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.51 3.80 Search for helices and strands: 0 residues in 0 chains, 7209 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 7224 seeds are put forward Round 1: 386 peptides, 80 chains. Longest chain 10 peptides. Score 0.288 Round 2: 481 peptides, 84 chains. Longest chain 14 peptides. Score 0.416 Round 3: 472 peptides, 76 chains. Longest chain 17 peptides. Score 0.455 Round 4: 472 peptides, 74 chains. Longest chain 18 peptides. Score 0.468 Round 5: 449 peptides, 73 chains. Longest chain 14 peptides. Score 0.440 Taking the results from Round 4 Chains 77, Residues 398, Estimated correctness of the model 0.0 % 4 chains (29 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 16134 restraints for refining 7141 atoms. 14512 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3103 (Rfree = 0.000) for 7141 atoms. Found 39 (39 requested) and removed 79 (19 requested) atoms. Cycle 17: After refmac, R = 0.3027 (Rfree = 0.000) for 7037 atoms. Found 39 (39 requested) and removed 50 (19 requested) atoms. Cycle 18: After refmac, R = 0.2810 (Rfree = 0.000) for 6979 atoms. Found 38 (38 requested) and removed 42 (19 requested) atoms. Cycle 19: After refmac, R = 0.2848 (Rfree = 0.000) for 6916 atoms. Found 38 (38 requested) and removed 25 (19 requested) atoms. Cycle 20: After refmac, R = 0.2679 (Rfree = 0.000) for 6900 atoms. Found 38 (38 requested) and removed 27 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.80 Search for helices and strands: 0 residues in 0 chains, 7168 seeds are put forward NCS extension: 24 residues added (2 deleted due to clashes), 7192 seeds are put forward Round 1: 369 peptides, 78 chains. Longest chain 9 peptides. Score 0.273 Round 2: 421 peptides, 79 chains. Longest chain 17 peptides. Score 0.355 Round 3: 419 peptides, 73 chains. Longest chain 18 peptides. Score 0.393 Round 4: 453 peptides, 76 chains. Longest chain 14 peptides. Score 0.426 Round 5: 434 peptides, 69 chains. Longest chain 17 peptides. Score 0.444 Taking the results from Round 5 Chains 70, Residues 365, Estimated correctness of the model 0.0 % 5 chains (31 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9891 reflections ( 98.93 % complete ) and 16623 restraints for refining 7238 atoms. 15138 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3066 (Rfree = 0.000) for 7238 atoms. Found 39 (39 requested) and removed 80 (19 requested) atoms. Cycle 22: After refmac, R = 0.3000 (Rfree = 0.000) for 7104 atoms. Found 39 (39 requested) and removed 42 (19 requested) atoms. Cycle 23: After refmac, R = 0.2843 (Rfree = 0.000) for 7047 atoms. Found 39 (39 requested) and removed 34 (19 requested) atoms. Cycle 24: After refmac, R = 0.1992 (Rfree = 0.000) for 7002 atoms. Found 38 (38 requested) and removed 24 (19 requested) atoms. Cycle 25: After refmac, R = 0.1747 (Rfree = 0.000) for 6991 atoms. Found 38 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.86 Search for helices and strands: 0 residues in 0 chains, 7258 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 7281 seeds are put forward Round 1: 366 peptides, 82 chains. Longest chain 9 peptides. Score 0.238 Round 2: 429 peptides, 84 chains. Longest chain 10 peptides. Score 0.333 Round 3: 448 peptides, 81 chains. Longest chain 14 peptides. Score 0.385 Round 4: 442 peptides, 79 chains. Longest chain 12 peptides. Score 0.389 Round 5: 445 peptides, 79 chains. Longest chain 12 peptides. Score 0.394 Taking the results from Round 5 Chains 80, Residues 366, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 9891 reflections ( 98.93 % complete ) and 16237 restraints for refining 7149 atoms. 14789 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2921 (Rfree = 0.000) for 7149 atoms. Found 39 (39 requested) and removed 75 (19 requested) atoms. Cycle 27: After refmac, R = 0.2849 (Rfree = 0.000) for 7039 atoms. Found 39 (39 requested) and removed 54 (19 requested) atoms. Cycle 28: After refmac, R = 0.2843 (Rfree = 0.000) for 6975 atoms. Found 38 (38 requested) and removed 34 (19 requested) atoms. Cycle 29: After refmac, R = 0.2831 (Rfree = 0.000) for 6939 atoms. Found 38 (38 requested) and removed 28 (19 requested) atoms. Cycle 30: After refmac, R = 0.1987 (Rfree = 0.000) for 6906 atoms. Found 38 (38 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.55 3.85 Search for helices and strands: 0 residues in 0 chains, 7167 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 7180 seeds are put forward Round 1: 313 peptides, 69 chains. Longest chain 7 peptides. Score 0.239 Round 2: 416 peptides, 83 chains. Longest chain 11 peptides. Score 0.318 Round 3: 455 peptides, 84 chains. Longest chain 15 peptides. Score 0.376 Round 4: 435 peptides, 79 chains. Longest chain 12 peptides. Score 0.378 Round 5: 431 peptides, 76 chains. Longest chain 17 peptides. Score 0.392 Taking the results from Round 5 Chains 79, Residues 355, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 16034 restraints for refining 7096 atoms. 14617 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2851 (Rfree = 0.000) for 7096 atoms. Found 39 (39 requested) and removed 59 (19 requested) atoms. Cycle 32: After refmac, R = 0.2788 (Rfree = 0.000) for 7006 atoms. Found 38 (38 requested) and removed 37 (19 requested) atoms. Cycle 33: After refmac, R = 0.2725 (Rfree = 0.000) for 6953 atoms. Found 38 (38 requested) and removed 30 (19 requested) atoms. Cycle 34: After refmac, R = 0.1994 (Rfree = 0.000) for 6925 atoms. Found 38 (38 requested) and removed 26 (19 requested) atoms. Cycle 35: After refmac, R = 0.2419 (Rfree = 0.000) for 6917 atoms. Found 38 (38 requested) and removed 27 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 3.83 Search for helices and strands: 0 residues in 0 chains, 7197 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 7213 seeds are put forward Round 1: 308 peptides, 70 chains. Longest chain 10 peptides. Score 0.222 Round 2: 393 peptides, 78 chains. Longest chain 10 peptides. Score 0.315 Round 3: 394 peptides, 71 chains. Longest chain 10 peptides. Score 0.367 Round 4: 394 peptides, 73 chains. Longest chain 12 peptides. Score 0.352 Round 5: 394 peptides, 68 chains. Longest chain 13 peptides. Score 0.388 Taking the results from Round 5 Chains 68, Residues 326, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 16069 restraints for refining 6988 atoms. 14817 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2971 (Rfree = 0.000) for 6988 atoms. Found 38 (38 requested) and removed 65 (19 requested) atoms. Cycle 37: After refmac, R = 0.2555 (Rfree = 0.000) for 6910 atoms. Found 38 (38 requested) and removed 48 (19 requested) atoms. Cycle 38: After refmac, R = 0.2766 (Rfree = 0.000) for 6871 atoms. Found 37 (37 requested) and removed 40 (18 requested) atoms. Cycle 39: After refmac, R = 0.2632 (Rfree = 0.000) for 6844 atoms. Found 37 (37 requested) and removed 27 (18 requested) atoms. Cycle 40: After refmac, R = 0.2759 (Rfree = 0.000) for 6842 atoms. Found 37 (37 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.80 Search for helices and strands: 0 residues in 0 chains, 7094 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 7105 seeds are put forward Round 1: 254 peptides, 56 chains. Longest chain 8 peptides. Score 0.229 Round 2: 322 peptides, 58 chains. Longest chain 17 peptides. Score 0.340 Round 3: 326 peptides, 60 chains. Longest chain 11 peptides. Score 0.331 Round 4: 322 peptides, 56 chains. Longest chain 17 peptides. Score 0.355 Round 5: 328 peptides, 60 chains. Longest chain 10 peptides. Score 0.335 Taking the results from Round 4 Chains 58, Residues 266, Estimated correctness of the model 0.0 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 15782 restraints for refining 6983 atoms. 14660 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3045 (Rfree = 0.000) for 6983 atoms. Found 38 (38 requested) and removed 73 (19 requested) atoms. Cycle 42: After refmac, R = 0.3043 (Rfree = 0.000) for 6900 atoms. Found 38 (38 requested) and removed 46 (19 requested) atoms. Cycle 43: After refmac, R = 0.3027 (Rfree = 0.000) for 6846 atoms. Found 37 (37 requested) and removed 33 (18 requested) atoms. Cycle 44: After refmac, R = 0.2141 (Rfree = 0.000) for 6810 atoms. Found 37 (37 requested) and removed 25 (18 requested) atoms. Cycle 45: After refmac, R = 0.1866 (Rfree = 0.000) for 6803 atoms. Found 37 (37 requested) and removed 19 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.87 Search for helices and strands: 0 residues in 0 chains, 7038 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 7053 seeds are put forward Round 1: 242 peptides, 57 chains. Longest chain 8 peptides. Score 0.196 Round 2: 296 peptides, 61 chains. Longest chain 12 peptides. Score 0.269 Round 3: 295 peptides, 60 chains. Longest chain 11 peptides. Score 0.275 Round 4: 325 peptides, 63 chains. Longest chain 12 peptides. Score 0.307 Round 5: 322 peptides, 63 chains. Longest chain 10 peptides. Score 0.302 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 63, Residues 262, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2pbl-3_warpNtrace.pdb as input Building loops using Loopy2018 63 chains (262 residues) following loop building 4 chains (16 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9891 reflections ( 98.93 % complete ) and 15421 restraints for refining 6755 atoms. 14393 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2761 (Rfree = 0.000) for 6755 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2769 (Rfree = 0.000) for 6697 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2707 (Rfree = 0.000) for 6652 atoms. Found 0 (36 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.1946 (Rfree = 0.000) for 6617 atoms. TimeTaking 75.13