Mon 24 Dec 07:34:55 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 2od6-1.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2od6-1.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2od6-1.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-1.8-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/2od6-1.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-1.8-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 07:35:00 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/2od6-1.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2od6-1.8-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 437 and 0 Target number of residues in the AU: 437 Target solvent content: 0.5168 Checking the provided sequence file Detected sequence length: 110 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 440 Adjusted target solvent content: 0.51 Input MTZ file: 2od6-1.8-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: 19 Cell parameters: 36.403 92.834 144.837 90.000 90.000 90.000 Input sequence file: 2od6-1.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 3520 target number of atoms Had to go as low as 0.45 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 1 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: 29.066 1.849 Wilson plot Bfac: 27.04 42951 reflections ( 99.78 % complete ) and 0 restraints for refining 3884 atoms. Observations/parameters ratio is 2.76 ------------------------------------------------------ Starting model: R = 0.3421 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3177 (Rfree = 0.000) for 3884 atoms. Found 89 (166 requested) and removed 91 (83 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.13 2.10 NCS extension: 0 residues added, 3882 seeds are put forward Round 1: 315 peptides, 38 chains. Longest chain 29 peptides. Score 0.663 Round 2: 343 peptides, 26 chains. Longest chain 36 peptides. Score 0.804 Round 3: 356 peptides, 21 chains. Longest chain 72 peptides. Score 0.849 Round 4: 367 peptides, 20 chains. Longest chain 78 peptides. Score 0.865 Round 5: 373 peptides, 20 chains. Longest chain 72 peptides. Score 0.870 Taking the results from Round 5 Chains 23, Residues 353, Estimated correctness of the model 98.7 % 10 chains (275 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 A and 60 A 21 chains (358 residues) following loop building 9 chains (281 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 4587 restraints for refining 3599 atoms. 1915 conditional restraints added. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3147 (Rfree = 0.000) for 3599 atoms. Found 123 (154 requested) and removed 81 (77 requested) atoms. Cycle 2: After refmac, R = 0.2911 (Rfree = 0.000) for 3628 atoms. Found 80 (153 requested) and removed 28 (78 requested) atoms. Cycle 3: After refmac, R = 0.2781 (Rfree = 0.000) for 3676 atoms. Found 52 (154 requested) and removed 24 (78 requested) atoms. Cycle 4: After refmac, R = 0.2710 (Rfree = 0.000) for 3696 atoms. Found 42 (155 requested) and removed 13 (79 requested) atoms. Cycle 5: After refmac, R = 0.2653 (Rfree = 0.000) for 3722 atoms. Found 39 (156 requested) and removed 21 (79 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.13 2.10 NCS extension: 11 residues added (34 deleted due to clashes), 3758 seeds are put forward Round 1: 383 peptides, 18 chains. Longest chain 72 peptides. Score 0.887 Round 2: 387 peptides, 14 chains. Longest chain 78 peptides. Score 0.907 Round 3: 390 peptides, 13 chains. Longest chain 76 peptides. Score 0.913 Round 4: 397 peptides, 14 chains. Longest chain 74 peptides. Score 0.913 Round 5: 396 peptides, 11 chains. Longest chain 92 peptides. Score 0.924 Taking the results from Round 5 Chains 14, Residues 385, Estimated correctness of the model 99.5 % 9 chains (356 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 15 A and 19 A Built loop between residues 20 C and 23 C Built loop between residues 31 D and 34 D 10 chains (391 residues) following loop building 6 chains (363 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 4135 restraints for refining 3785 atoms. 991 conditional restraints added. Observations/parameters ratio is 2.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2686 (Rfree = 0.000) for 3785 atoms. Found 114 (156 requested) and removed 85 (81 requested) atoms. Cycle 7: After refmac, R = 0.2528 (Rfree = 0.000) for 3803 atoms. Found 94 (153 requested) and removed 36 (81 requested) atoms. Cycle 8: After refmac, R = 0.2412 (Rfree = 0.000) for 3856 atoms. Found 77 (155 requested) and removed 20 (82 requested) atoms. Cycle 9: After refmac, R = 0.2354 (Rfree = 0.000) for 3900 atoms. Found 68 (157 requested) and removed 29 (83 requested) atoms. Cycle 10: After refmac, R = 0.2304 (Rfree = 0.000) for 3936 atoms. Found 69 (158 requested) and removed 20 (84 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.13 2.10 NCS extension: 19 residues added (42 deleted due to clashes), 4008 seeds are put forward Round 1: 405 peptides, 9 chains. Longest chain 106 peptides. Score 0.935 Round 2: 409 peptides, 7 chains. Longest chain 106 peptides. Score 0.943 Round 3: 404 peptides, 7 chains. Longest chain 106 peptides. Score 0.941 Round 4: 408 peptides, 7 chains. Longest chain 107 peptides. Score 0.943 Round 5: 413 peptides, 6 chains. Longest chain 107 peptides. Score 0.948 Taking the results from Round 5 Chains 7, Residues 407, Estimated correctness of the model 99.8 % 6 chains (404 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 92 A 6 chains (409 residues) following loop building 5 chains (406 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 3858 restraints for refining 3915 atoms. 456 conditional restraints added. Observations/parameters ratio is 2.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2438 (Rfree = 0.000) for 3915 atoms. Found 104 (157 requested) and removed 87 (83 requested) atoms. Cycle 12: After refmac, R = 0.2343 (Rfree = 0.000) for 3928 atoms. Found 73 (155 requested) and removed 31 (84 requested) atoms. Cycle 13: After refmac, R = 0.2276 (Rfree = 0.000) for 3964 atoms. Found 61 (156 requested) and removed 17 (85 requested) atoms. Cycle 14: After refmac, R = 0.2231 (Rfree = 0.000) for 4002 atoms. Found 67 (157 requested) and removed 27 (85 requested) atoms. Cycle 15: After refmac, R = 0.2232 (Rfree = 0.000) for 4028 atoms. Found 82 (159 requested) and removed 35 (86 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.13 2.10 NCS extension: 12 residues added (15 deleted due to clashes), 4089 seeds are put forward Round 1: 421 peptides, 6 chains. Longest chain 106 peptides. Score 0.951 Round 2: 420 peptides, 8 chains. Longest chain 108 peptides. Score 0.945 Round 3: 413 peptides, 9 chains. Longest chain 108 peptides. Score 0.939 Round 4: 421 peptides, 7 chains. Longest chain 108 peptides. Score 0.948 Round 5: 414 peptides, 13 chains. Longest chain 82 peptides. Score 0.926 Taking the results from Round 1 Chains 7, Residues 415, Estimated correctness of the model 99.8 % 5 chains (409 residues) have been docked in sequence Building loops using Loopy2018 7 chains (415 residues) following loop building 5 chains (409 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 3819 restraints for refining 3947 atoms. 386 conditional restraints added. Observations/parameters ratio is 2.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2351 (Rfree = 0.000) for 3947 atoms. Found 123 (155 requested) and removed 76 (84 requested) atoms. Cycle 17: After refmac, R = 0.2277 (Rfree = 0.000) for 3986 atoms. Found 85 (154 requested) and removed 25 (85 requested) atoms. Cycle 18: After refmac, R = 0.2228 (Rfree = 0.000) for 4044 atoms. Found 81 (156 requested) and removed 28 (86 requested) atoms. Cycle 19: After refmac, R = 0.2189 (Rfree = 0.000) for 4091 atoms. Found 63 (157 requested) and removed 36 (87 requested) atoms. Cycle 20: After refmac, R = 0.2149 (Rfree = 0.000) for 4111 atoms. Found 72 (155 requested) and removed 27 (88 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.13 2.10 NCS extension: 16 residues added (17 deleted due to clashes), 4173 seeds are put forward Round 1: 417 peptides, 7 chains. Longest chain 106 peptides. Score 0.947 Round 2: 416 peptides, 7 chains. Longest chain 106 peptides. Score 0.946 Round 3: 410 peptides, 10 chains. Longest chain 106 peptides. Score 0.934 Round 4: 417 peptides, 9 chains. Longest chain 106 peptides. Score 0.940 Round 5: 414 peptides, 10 chains. Longest chain 106 peptides. Score 0.936 Taking the results from Round 1 Chains 7, Residues 410, Estimated correctness of the model 99.7 % 6 chains (407 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 83 A and 94 A Built loop between residues 54 C and 57 C 4 chains (419 residues) following loop building 4 chains (419 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 3929 restraints for refining 4046 atoms. 433 conditional restraints added. Observations/parameters ratio is 2.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2401 (Rfree = 0.000) for 4046 atoms. Found 107 (152 requested) and removed 88 (86 requested) atoms. Cycle 22: After refmac, R = 0.2294 (Rfree = 0.000) for 4043 atoms. Found 99 (150 requested) and removed 46 (87 requested) atoms. Cycle 23: After refmac, R = 0.2242 (Rfree = 0.000) for 4093 atoms. Found 77 (150 requested) and removed 32 (87 requested) atoms. Cycle 24: After refmac, R = 0.2204 (Rfree = 0.000) for 4129 atoms. Found 71 (152 requested) and removed 27 (88 requested) atoms. Cycle 25: After refmac, R = 0.2160 (Rfree = 0.000) for 4163 atoms. Found 80 (153 requested) and removed 34 (89 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.13 2.10 NCS extension: 11 residues added (13 deleted due to clashes), 4224 seeds are put forward Round 1: 408 peptides, 7 chains. Longest chain 106 peptides. Score 0.943 Round 2: 406 peptides, 8 chains. Longest chain 106 peptides. Score 0.939 Round 3: 404 peptides, 9 chains. Longest chain 106 peptides. Score 0.935 Round 4: 407 peptides, 9 chains. Longest chain 106 peptides. Score 0.936 Round 5: 407 peptides, 9 chains. Longest chain 106 peptides. Score 0.936 Taking the results from Round 1 Chains 7, Residues 401, Estimated correctness of the model 99.7 % 6 chains (397 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 C and 60 C 6 chains (405 residues) following loop building 5 chains (401 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 4115 restraints for refining 4031 atoms. 753 conditional restraints added. Observations/parameters ratio is 2.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2363 (Rfree = 0.000) for 4031 atoms. Found 107 (148 requested) and removed 87 (86 requested) atoms. Cycle 27: After refmac, R = 0.2278 (Rfree = 0.000) for 4047 atoms. Found 82 (145 requested) and removed 19 (86 requested) atoms. Cycle 28: After refmac, R = 0.2219 (Rfree = 0.000) for 4105 atoms. Found 70 (148 requested) and removed 28 (88 requested) atoms. Cycle 29: After refmac, R = 0.2188 (Rfree = 0.000) for 4139 atoms. Found 70 (149 requested) and removed 17 (88 requested) atoms. Cycle 30: After refmac, R = 0.2180 (Rfree = 0.000) for 4183 atoms. Found 53 (150 requested) and removed 40 (89 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.13 2.10 NCS extension: 29 residues added (23 deleted due to clashes), 4225 seeds are put forward Round 1: 407 peptides, 10 chains. Longest chain 108 peptides. Score 0.933 Round 2: 410 peptides, 8 chains. Longest chain 108 peptides. Score 0.941 Round 3: 410 peptides, 10 chains. Longest chain 108 peptides. Score 0.934 Round 4: 410 peptides, 11 chains. Longest chain 105 peptides. Score 0.931 Round 5: 401 peptides, 10 chains. Longest chain 108 peptides. Score 0.930 Taking the results from Round 2 Chains 8, Residues 402, Estimated correctness of the model 99.7 % 5 chains (386 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 A and 59 A 7 chains (404 residues) following loop building 4 chains (388 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 4129 restraints for refining 4000 atoms. 820 conditional restraints added. Observations/parameters ratio is 2.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2326 (Rfree = 0.000) for 4000 atoms. Found 129 (140 requested) and removed 66 (85 requested) atoms. Cycle 32: After refmac, R = 0.2246 (Rfree = 0.000) for 4053 atoms. Found 79 (139 requested) and removed 26 (87 requested) atoms. Cycle 33: After refmac, R = 0.2201 (Rfree = 0.000) for 4100 atoms. Found 71 (140 requested) and removed 25 (87 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2159 (Rfree = 0.000) for 4143 atoms. Found 63 (142 requested) and removed 31 (88 requested) atoms. Cycle 35: After refmac, R = 0.2139 (Rfree = 0.000) for 4167 atoms. Found 60 (142 requested) and removed 26 (89 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.13 2.10 NCS extension: 26 residues added (28 deleted due to clashes), 4227 seeds are put forward Round 1: 410 peptides, 8 chains. Longest chain 108 peptides. Score 0.941 Round 2: 416 peptides, 6 chains. Longest chain 108 peptides. Score 0.949 Round 3: 407 peptides, 9 chains. Longest chain 89 peptides. Score 0.936 Round 4: 416 peptides, 7 chains. Longest chain 108 peptides. Score 0.946 Round 5: 410 peptides, 7 chains. Longest chain 108 peptides. Score 0.944 Taking the results from Round 2 Chains 6, Residues 410, Estimated correctness of the model 99.8 % 6 chains (410 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 94 A and 97 A 5 chains (412 residues) following loop building 5 chains (412 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 3891 restraints for refining 4039 atoms. 459 conditional restraints added. Observations/parameters ratio is 2.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2301 (Rfree = 0.000) for 4039 atoms. Found 123 (138 requested) and removed 77 (86 requested) atoms. Cycle 37: After refmac, R = 0.2224 (Rfree = 0.000) for 4069 atoms. Found 99 (136 requested) and removed 21 (87 requested) atoms. Cycle 38: After refmac, R = 0.2178 (Rfree = 0.000) for 4142 atoms. Found 69 (138 requested) and removed 47 (88 requested) atoms. Cycle 39: After refmac, R = 0.2157 (Rfree = 0.000) for 4160 atoms. Found 69 (135 requested) and removed 34 (89 requested) atoms. Cycle 40: After refmac, R = 0.2137 (Rfree = 0.000) for 4187 atoms. Found 73 (136 requested) and removed 47 (89 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.12 2.09 NCS extension: 16 residues added (18 deleted due to clashes), 4230 seeds are put forward Round 1: 412 peptides, 7 chains. Longest chain 107 peptides. Score 0.945 Round 2: 412 peptides, 8 chains. Longest chain 106 peptides. Score 0.941 Round 3: 412 peptides, 10 chains. Longest chain 108 peptides. Score 0.935 Round 4: 406 peptides, 9 chains. Longest chain 108 peptides. Score 0.936 Round 5: 408 peptides, 11 chains. Longest chain 106 peptides. Score 0.930 Taking the results from Round 1 Chains 7, Residues 405, Estimated correctness of the model 99.7 % 7 chains (405 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 94 A and 97 A Built loop between residues 24 D and 27 D 5 chains (409 residues) following loop building 5 chains (409 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 3939 restraints for refining 4042 atoms. 525 conditional restraints added. Observations/parameters ratio is 2.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2313 (Rfree = 0.000) for 4042 atoms. Found 128 (128 requested) and removed 80 (86 requested) atoms. Cycle 42: After refmac, R = 0.2225 (Rfree = 0.000) for 4080 atoms. Found 109 (126 requested) and removed 23 (87 requested) atoms. Cycle 43: After refmac, R = 0.2161 (Rfree = 0.000) for 4160 atoms. Found 77 (128 requested) and removed 26 (89 requested) atoms. Cycle 44: After refmac, R = 0.2121 (Rfree = 0.000) for 4207 atoms. Found 62 (130 requested) and removed 31 (90 requested) atoms. Cycle 45: After refmac, R = 0.2095 (Rfree = 0.000) for 4227 atoms. Found 69 (130 requested) and removed 32 (90 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.13 2.10 NCS extension: 11 residues added (16 deleted due to clashes), 4275 seeds are put forward Round 1: 411 peptides, 7 chains. Longest chain 107 peptides. Score 0.944 Round 2: 414 peptides, 6 chains. Longest chain 107 peptides. Score 0.948 Round 3: 410 peptides, 7 chains. Longest chain 106 peptides. Score 0.944 Round 4: 412 peptides, 6 chains. Longest chain 107 peptides. Score 0.948 Round 5: 408 peptides, 8 chains. Longest chain 107 peptides. Score 0.940 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 406, Estimated correctness of the model 99.8 % 6 chains (404 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 90 D and 94 D 6 chains (408 residues) following loop building 5 chains (407 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 42951 reflections ( 99.78 % complete ) and 3405 restraints for refining 3335 atoms. Observations/parameters ratio is 3.22 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2869 (Rfree = 0.000) for 3335 atoms. Found 54 (102 requested) and removed 0 (102 requested) atoms. Cycle 47: After refmac, R = 0.2709 (Rfree = 0.000) for 3335 atoms. Found 29 (104 requested) and removed 4 (72 requested) atoms. Cycle 48: After refmac, R = 0.2601 (Rfree = 0.000) for 3335 atoms. Found 21 (105 requested) and removed 3 (73 requested) atoms. Cycle 49: After refmac, R = 0.2538 (Rfree = 0.000) for 3335 atoms. TimeTaking 56.22